Thermo SpectraSYSTEM AS3000 Autosampler

SpectraSYSTEM
AS3000 Autosampler
(with column oven and tray temperature control)
User Guide
A0099-97006 Revision A June 2010
© 2010 Thermo Fisher Scientific Inc. All rights reserved.
SpectraSYSTEM, SpectraNET, and PushLoop are trademarks of Thermo Fisher Scientific Inc. in the United
States.
Tygon is a registered trademark of Saint-Gobain Performance Plastics Company in the United States and
possibly other countries.
Teflon is a registered trademark of E.I. du Pont de Nemours & Company in the United States and other
countries.
Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Revision A, released June 2010
For Research Use Only. Not for use in diagnostic procedures.

Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section.
Changes that you make to your system might void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
SpectraSYSTEM AS3000
(with oven and tray temperature control)
EMC Directive 2004/108/EC
EMC compliance has been evaluated by TÜV Rheinland of North America.
EN 55011: 2007; A2:2007 EN 61000-4-4: 2004

EN 61000-3-2: 2006 EN 61000-4-5: 2005
EN 61000-3-3: 1995, A1: 2001, A2: 2005 EN 61000-4-6: 2007
EN 61000-4-2: 1995, A1: 1999, A2: 2001 EN 61000-4-11: 2004
EN 61000-4-3: 2006 EN 61326-1: 2006
FCC Class A: CFR 47: Part 15: 2009
Low Voltage Safety Compliance

Low voltage safety compliance has been evaluated by TÜV Rheinland of North America.
This device complies with Low Voltage Directive 2006/95/EC, harmonized standard EN 61010-1: 2001,
IEC 61010-1: 2002, UL 61010A-1: 2004, and CAN/CSA 22.2 61010-1: 2004.
Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
FCC Compliance Statement
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Notice on Lifting and Handling of

Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too bulky for one person alone
to lift or move safely.
Notice on the Proper Use of

Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.
Notice on the Susceptibility

to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.

WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:
Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermo.com/
WEEERoHS for further information on Thermo Fisher Scientific’s compliance with these Directives and the
recyclers in your country.
WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen.
Das Produkt ist durch folgendes Symbol gekennzeichnet:
Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise,
die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermo.com/WEEERoHS.
Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:
Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermo.com/WEEERoHS.
CAUTION Symbol CAUTION VORSICHT ATTENTION PRECAUCION AVVERTENZA
Electric Shock: This instrument uses Elektroschock: In diesem Gerät werden Choc électrique: L’instrument utilise des Descarga eléctrica: Este instrumento Shock da folgorazione. L’apparecchio è
high voltages that can cause personal Hochspannungen verwendet, die tensions capables d’infliger des blessures utiliza altas tensiones, capaces de alimentato da corrente ad alta tensione
injury. Before servicing, shut down the Verletzungen verursachen können. Vor corporelles. L’instrument doit être arrêté et producir lesiones personales. Antes de che puo provocare lesioni fisiche. Prima di
instrument and disconnect the instrument Wartungsarbeiten muß das Gerät débranché de la source de courant avant dar servicio de mantenimiento al effettuare qualsiasi intervento di
from line power. Keep the top cover on abgeschaltet und vom Netz getrennt tout intervention. Ne pas utiliser instrumento, éste debera apagarse y manutenzione occorre spegnere ed isolare
while operating the instrument. Do not werden. Betreiben Sie Wartungsarbeiten l’instrument sans son couvercle. Ne pas desconectarse de la línea de alimentacion l’apparecchio dalla linea elettrica. Non
remove protective covers from PCBs. nicht mit abgenommenem Deckel. Nehmen enlever les étuis protecteurs des cartes de eléctrica. No opere el instrumento sin sus attivare lo strumento senza lo schermo
Sie die Schutzabdeckung von Leiterplatten circuits imprimés. cubiertas exteriores quitadas. No remueva superiore. Non togliere i coperchi a
nicht ab. las cubiertas protectoras de las tarjetas protezione dalle schede di circuito
de circuito impreso. stampato (PCB).
Chemical: This instrument might contain Chemikalien: Dieses Gerät kann Chimique: Des produits chimiques Química: El instrumento puede contener Prodotti chimici. Possibile presenza di
hazardous chemicals. Wear gloves when gefährliche Chemikalien enthalten. Tragen dangereux peuvent se trouver dans productos quimicos peligrosos. Utilice sostanze chimiche pericolose
handling toxic, carcinogenic, mutagenic, Sie Schutzhandschuhe beim Umgang mit l’instrument. Portez des gants pour guantes al manejar productos quimicos nell’apparecchio. Indossare dei guanti per
or corrosive or irritant chemicals. Use toxischen, karzinogenen, mutagenen oder manipuler tous produits chimiques tóxicos, carcinogenos, mutagenos o maneggiare prodotti chimici tossici,
approved containers and proper ätzenden/reizenden Chemikalien. toxiques, cancérigènes, mutagènes, ou corrosivos/irritantes. Utilice recipientes y cancerogeni, mutageni, o
procedures to dispose waste oil. Entsorgen Sie verbrauchtes Öl corrosifs/irritants. Utiliser des récipients procedimientos aprobados para corrosivi/irritanti. Utilizzare contenitori
entsprechend den Vorschriften in den et des procédures homologuées pour se deshacerse del aceite usado. aprovo e seguire la procedura indicata per
vorgeschriebenen Behältern. débarrasser des déchets d’huile. lo smaltimento dei residui di olio.
Heat: Before servicing the instrument, Hitze: Warten Sie erhitzte Komponenten Haute Temperature: Permettre aux Altas temperaturas: Permita que lop Calore. Attendere che i componenti
allow any heated components to cool. erst nachdem diese sich abgekühlt haben. composants chauffés de refroidir avant componentes se enfríen, ante de efectuar riscaldati si raffreddino prima di
tout intervention. servicio de mantenimiento. effetturare l’intervento di manutenzione.
Fire: Use care when operating the system Feuer: Beachten Sie die einschlägigen Incendie: Agir avec précaution lors de Fuego: Tenga cuidado al operar el Incendio. Adottare le dovute precauzioni
in the presence of flammable gases. VorsichtsmaBnahmen, wenn Sie das l’utilisation du système en présence de sistema en presencia de gases quando si usa il sistema in presenza di gas
System in Gegenwart von entzündbaren gaz inflammables. inflamables. infiammabili.
Gasen betreiben.
Eye Hazard: Eye damage could occur Verletzungsgefahr der Augen: Danger pour les yeux: Des projections Peligro par los ojos: Las salicaduras de Pericolo per la vista. Gli schizzi di
from splattered chemicals or flying Verspritzte Chemikalien oder kleine chimiques, liquides, ou solides peuvent productos químicos o particulas que prodotti chimici o delle particelle presenti
particles. Wear safety glasses when Partikel können Augenverletzungen être dangereuses pour les yeux. Porter des salten bruscamente pueden causar nell’aria potrebbero causare danni alla
handling chemicals or servicing the verursachen. Tragen Sie beim Umgang mit lunettes de protection lors de toute lesiones en los ojos. Utilice anteojos vista. Indossare occhiali protettivi quando
instrument. Chemikalien oder bei der Wartung des manipulation de produit chimique ou pour protectores al mnipular productos si maneggiano prodotti chimici o si
Gerätes eine Schutzbrille. toute intervention sur l’instrument. químicos o al darle servicio de effettuano interventi di manutenzione
mantenimiento al instrumento. sull’apparecchio.
General Hazard: A hazard is present that Allgemeine Gefahr: Es besteht eine Danger général: Indique la présence Peligro general: Significa que existe un Pericolo generico. Pericolo non
is not included in the above categories. weitere Gefahr, die nicht in den d’un risque n’appartenant pas aux peligro no incluido en las categorias compreso tra le precedenti categorie.
Also, this symbol appears on the vorstehenden Kategorien beschrieben ist. catégories citées plus haut. Ce symbole anteriores. Este simbolo también se utiliza Questo simbolo è utilizzato inoltre
instrument to refer the user to instructions Dieses Symbol wird im Handbuch figure également sur l’instrument pour en el instrumento par referir al usuario a sull’apparecchio per segnalare all’utente
in this manual. auBerdem dazu verwendet, um den renvoyer l’utilisateur aux instructions du las instrucciones contenidas en este di consultare le istruzioni descritte nel
Benutzer auf Anweisungen hinzuweisen. présent manuel. manual. presente manuale.
When the safety of a procedure is Wenn Sie sich über die Sicherheit eines Si la sûreté d’une procédure est Cuando la certidumbre acerca de un Quando e in dubbio la misura di sicurezza
questionable, contact your local Technical Verfahrens im unklaren sind, setzen Sie incertaine, avant de continuer, contacter procedimiento sea dudosa, antes de per una procedura, prima di continuare, si
Support organization for Thermo Fisher sich, bevor Sie fortfahren, mit Ihrer le plus proche Service Clientèle pour les proseguir, pongase en contacto con la prega di mettersi in contatto con il
Scientific San Jose Products. lokalen technischen produits de Thermo Fisher Scientific San Oficina de Asistencia Tecnica local para Servizio di Assistenza Tecnica locale per i
Unterstützungsorganisation für Thermo Jose. los productos de Thermo Fisher Scientific prodotti di Thermo Fisher Scientific San
Fisher Scientific San Jose Produkte in San Jose. Jose.
Verbindung.
CAUTION Symbol CAUTION
Electric Shock: This instrument uses

high voltages that can cause personal
injury. Before servicing, shut down the
instrument and disconnect the instrument
from line power. Keep the top cover on
while operating the instrument. Do not
remove protective covers from PCBs.
Chemical: This instrument might contain

hazardous chemicals. Wear gloves when
handling toxic, carcinogenic, mutagenic,
or corrosive or irritant chemicals. Use
approved containers and proper
procedures to dispose waste oil.
Heat: Before servicing the instrument,

allow any heated components to cool.
Fire: Use care when operating the system

in the presence of flammable gases.
Eye Hazard: Eye damage could occur

from splattered chemicals or flying
particles. Wear safety glasses when
handling chemicals or servicing the
instrument.
General Hazard: A hazard is present that

is not included in the above categories.
Also, this symbol appears on the
instrument to refer the user to instructions
in this manual.
When the safety of a procedure is

questionable, contact your local Technical
Support organization for Thermo Fisher
Scientific San Jose Products.
C
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Safety Precautions for the SpectraSYSTEM Autosampler . . . . . . . . . . . . . . . . .xiv
Good Laboratory Practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Functional Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Autosampler Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Injection Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Operation Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Manual Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Autosampler Displays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Text Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Standard Words. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Chapter 2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Startup Checklist. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Electrical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Lifting the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Unpacking the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Connecting the Autosampler to the Building Ground . . . . . . . . . . . . . . . . . . . . 19
Connecting the Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Connecting the Flush Solvent Bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Installing the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Connecting the Pump to the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Installing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Connecting the LC Column’s Outlet to the Detector’s Flowcell Inlet . . . . . . 26
Installing the Column Compartment Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Installing the Sample Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Powering-Up the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Priming the Autosampler. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide ix

Contents
Communication: SpectraNet or Stand Alone . . . . . . . . . . . . . . . . . . . . . . . . . . 30

SpectraNet Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Stand Alone Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Performance Verification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Reproducibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Sample Carryover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Chapter 3 Keypad Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Command Center . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Keypad Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Menus and Screens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Main Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Status Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
User Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Confirmation Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Chapter 4 Standalone Operation from the Command Center. . . . . . . . . . . . . . . . . . . . . . . . . .63

Run Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Creating a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Saving a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Loading a File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Building a Sample Queue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Entering Your Other LC Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Starting a Run by Pressing the Run Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Monitoring the Run Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Sample Queue Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Injection Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
File Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Temperature Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Changing the Run in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Priority Sample Sets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Stopping a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
File Management. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Saving Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Copying Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Deleting Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Protecting Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Changes to Real-Time Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Optimization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Injection Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Solvent Viscosity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Needle Height . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
x SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Contents
Special Commands in the Commands Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Flush Sample Syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Initialize Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Injector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Arm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Chapter 5 Diagnostic Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99

Gradient Delay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Calculating the Gradient Delay Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Gradient Delay Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Diagnostics in the Tests Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Interpreting the Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Test Descriptions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Chapter 6 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

Specific Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Maintenance Schedule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Maintenance Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Emptying the Flush-Solvent Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Replacing the Rotor Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Replacing the Flush Solvent Inlet Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Maintaining the Sample Needle Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Replacing the Syringe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Changing the Sample Loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Replacing the Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Automated Shutdown in the Stand Alone Mode . . . . . . . . . . . . . . . . . . . . . . . 123
Maintenance Log. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129

General Chromatography Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Autosampler Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Display Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
User Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Confirmation Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Testing for Tubing Restrictions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xi

Contents
Chapter 8 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .145

Clear Vials and Vial Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Amber Vials and Vial Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Cables and Adapters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Standard Autosamplers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Inert/Biocompatible Autosamplers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Test Mixes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Upgrade Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Appendix A Quick Reference Guides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .149

SpectraSYSTEM AS3000 Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
SpectraSYSTEM AS3000 Quick Reference Guide. . . . . . . . . . . . . . . . . . . . . . 153
Quick Start: Starting Runs from the Command Center. . . . . . . . . . . . . . . . . . 155
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .157
xii SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

P
Preface
This guide describes how to install, operate, and maintain the SpectraSYSTEM™ AS3000
autosampler, as well as how to inject samples and perform diagnostics from the front panel
keypad.
Contents
• Safety and Special Notices
• Safety Precautions for the SpectraSYSTEM Autosampler
• Good Laboratory Practices
• Contacting Us
Safety and Special Notices

This guide contains the following safety and special notices.
CAUTION Alerts you to situations that could result in personal injury and tells you how to
avoid them.
CAUTION High Voltage. Alerts you to the presence of high voltage and to the potential
injury that could occur from electrical shock if you came into contact with a specific
instrument area or component. Also indicates how to avoid contact with the high-voltage
areas in your instrument.
CAUTION Hot Surface. Alerts you to potential injury that could occur from contact with
a heated surface or area on or in an instrument. Also, tells you how to avoid contact with
the heated surfaces in your instrument.
CAUTION Alerts you to situations that could result in personal injury caused by lifting
objects that are too heavy, too bulky, or both.
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xiii

Preface
IMPORTANT Alerts you to connections to the building ground.
IMPORTANT Alerts you to grounding connections that require a protective earth ground.
IMPORTANT Alerts you to the correct operating or maintenance procedures needed to

prevent equipment or data damage. It also alerts you to important exceptions, side effects,
or unexpected occurrences that can result from certain actions.
Tip Calls out general rules or shortcuts. Tips specify ways to obtain the best performance
and results from your instrument.
Safety Precautions for the SpectraSYSTEM Autosampler

Follow these safety precautions for the SpectraSYSTEM autosampler.
Grounding Requirements
The SpectraSYSTEM autosampler requires two levels of grounding. When you install the
SpectraSYSTEM autosampler, connect the power cord to a power outlet with a protective
earth ground. In addition, connect the grounding post on the back panel of the autosampler
to the building ground (see “Connecting the Autosampler to the Building Ground” on
page 19).
IMPORTANT Make sure that the power cord is connected to a power outlet with a
protective earth ground.
IMPORTANT Make sure that the grounding post on the back panel of the autosampler is
connected to the building ground.
xiv SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Preface
High-Temperature Components
When you set the column oven to high temperatures, the compartment’s metal components
can cause burns. When you want to change the LC column or tighten the liquid connections
to the LC column, turn off the column oven, and wait for the oven to cool to room
temperature.
CAUTION Never touch the metal components of the column oven compartment when
you are operating the oven at high temperatures. The metal components can cause burns.
Heavy Lifting Hazard

Because the autosampler is bulky and heavy, lifting it requires a team effort. For information
on how to safely lift the autosampler, see “Lifting the Autosampler” on page 17.
CAUTION For your safety, and in compliance with international regulations, ask for
assistance when moving the autosampler from one benchtop location to another. The
autosampler is too bulky for one person alone to lift or move safely.
Good Laboratory Practices

To obtain optimal performance from your LC system and to prevent personal injury or injury
to the environment, do the following:
• Keep good records.
• Read the manufacturers’ Material Safety Data Sheets (MSDSs) for the chemicals being
used in your laboratory.
• Remove particulate matter from your samples before you inject them into the liquid
chromatograph.
• Use HPLC-grade solvents.
• Connect the drainage tubes from the pump, autosampler, and detector to an appropriate
waste receptacle. Dispose of solvents as specified by local regulations.
Keeping Good Records

To help identify and isolate problems with either your equipment or your methodology, keep
good records of all system conditions (for example,% RSDs on retention times and peak areas,
peak shape, and resolution). At a minimum, keep a chromatogram of a typical sample and
standard mixture, well documented with system conditions, for future reference. Careful
comparison of retention times, peak shapes, peak sensitivity, and baseline noise can provide
valuable clues to identifying and solving future problems.
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xv

Preface
Chemical Toxicity
Although the large volume of toxic and flammable solvents used and stored in laboratories can
be quite dangerous, do not ignore the potential hazards posed by your samples. Take special
care to read and follow all precautions that ensure proper ventilation, storage, handling, and
disposal of both solvents and samples. Become familiar with the toxicity data and potential
hazards associated with all chemicals by referring to the manufacturers’ MSDSs.
Sample Preparation
Always consider the solubility of your sample in the solvent/mobile phase. Sample
precipitation can plug the column, tubing, or flowcell causing flow restriction. This
obstruction can result in irreparable damage to the system. To avoid damage caused by
particulate matter, filter samples through 0.45 or 0.2 micron (or less) filters.
Solvent Requirements
Many chemical manufacturers provide a line of high-purity or HPLC-grade reagents that are
free of chemical impurities. Routine filtration of all solvents or eluents through a 0.45 or
0.2 micron (or less) fluorocarbon filter before placing them in the solvent reservoir
significantly prolongs the life and effectiveness of the inlet filters, check valves and seals,
injection valve, and column. Typically, HPLC-grade solvents do not require filtration.
Choose a mobile phase that is compatible with the sample and column you have selected for
your separation. Remember that some solvents are corrosive to stainless steel.
Solvent Disposal
Make sure you have a solvent waste container or other kind of drain system available at or
below the benchtop level. Most solvents have special disposal requirements and should not be
disposed of directly down a drain. Follow all governmental regulations when disposing of any
chemical.
High-Pressure Systems and Leaks

LC systems operate at high pressures. Because liquids are not highly compressible, they do not
store much energy. Accordingly, there is little immediate danger from the high pressures in an
LC system. However, if a leak occurs, correct it as soon as possible. Always wear eye and skin
protection when operating or maintaining an LC system. Always shut down the system and
return it to atmospheric pressure before attempting any maintenance.
xvi SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Preface
Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.
Y To contact Technical Support
Phone 800-532-4752
Fax 561-688-8736
E-mail us.techsupport.analyze@thermofisher.com
Knowledge base www.thermokb.com
Find software updates and utilities to download at mssupport.thermo.com.
Y To contact Customer Service for ordering information
Phone 800-532-4752
Fax 561-688-8731
E-mail us.customer-support.analyze@thermofisher.com
Web site www.thermo.com/ms
Y To copy manuals from the Internet
Go to http://sjsupport.thermofinnigan.com/public/index_download_customer.asp and
click Customer Manuals in the left margin of the window.
Y To suggest changes to documentation or to Help
• To provide us with comments about this document, click the link below. Thank you
in advance for your help.
• Send an e-mail message to the Technical Publications Editor at

techpubs-lcms@thermofisher.com.
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xvii

1
Introduction
This chapter introduces the Thermo Scientific SpectraSYSTEM AS3000 autosampler
(see Figure 1) and describes the conventions used in this manual.
Figure 1. SpectraSYSTEM AS3000 autosampler
Contents
• Functional Description
• Operation Modes
• Manual Conventions
• Specifications
Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide 1

1 Introduction
Functional Description
These topics describe the autosampler’s components and injection types:
• “Autosampler Components” on page 2
• “Injection Types” on page 4
• “Operation Modes” on page 8
Autosampler Components
The autosampler consists of the following components:
• Injection valve and sample loop
• XYZ arm with holding hook and needle
• Syringe and two-position syringe valve
• Tray compartment and temperature control unit
• Column oven compartment
Figure 2 shows the components of the autosampler's injection system.

Figure 2. Injection system
Flush
Sample solvent
syringe
valve
Needle
Sample vial
Injection Sample
Sample loop tower syringe
Injection valve
2
1 Pump output line
3
6
4
5
Column input line
Injection
Injection valve tower
2 SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

1 Introduction
Prior to sample analysis, the operator loads vials filled with samples and calibration standards
into three trays that hold 35 vials each if the tray temperature control unit is installed. During
operation, the autosampler’s mechanical arm (the XYZ arm) locates the requested vial. The
hook on the end of the arm moves under the selected vial and lifts it from the sample tray. The
XYZ arm transports the vial to the sample tower and the sample needle for sample injection.
As necessary, the injection valve switches between the inject and fill positions (see Figure 3) to
draw sample or solvent into the autosampler lines and to inject sample onto the column.
Figure 3. Inject and fill positions for the injection valve
Fill position Inject position
2 2
1 1
3 3
6 From 6 From
pump pump
4 4
5 To 5 To
column column
The tray compartment holds the sample trays, the injection tower, and the sample syringe.
The temperature control unit for the tray compartment consists of four Peltier devices, two
high-speed fans, and a heat sink. Heat is pumped from the sample compartment into the heat
sink and then blown out the back of the instrument by the two fans. A temperature sensor
sends the temperature reading back to the microprocessor, which controls the operation of the
four Peltier devices to regulate the sample compartment temperature. Similar to the column
oven, the tray temperature control unit is a closed assembly and requires no routine
maintenance.
Note The current version of the SpectraSYSTEM AS3000 autosampler includes a

temperature-control unit for the tray compartment and the vial trays hold 35 vials each.
The temperature-control unit maintains the temperature of the tray compartment

within ± 2 °C. At ambient room temperature, the tray compartment takes approximately
30 minutes to reach a temperature of 0 °C and approximately 10 minutes to reach a
temperature of 60 °C.
The actual temperature inside the autosampler vial depends on the specified tray temperature,
type of vial, sample buffer, and so on. Compared to the tray temperature, the vial temperature
tends to be higher below 30 °C and lower above 30 °C. The time lag in heating and cooling is
due to variations in ambient temperatures, indirect contact with temperature control units,
and vial type.
The column oven compartment holds the LC column. The column oven contains a resistive
thermal device that heats up to stabilize the column temperature. A temperature sensor
detects the temperature and sends the temperature reading back to the microprocessor, which
turns the resistive device on or off to regulate the temperature. This assembly is closed and
requires no routine maintenance.

1 Introduction
Injection Types
The SpectraSYSTEM AS3000 autosampler has three injection types:
• Full-loop Injection Type
• Pull-loop Injection Type
• PushLoop Injection Type
The pull-loop and PushLoop™ injection types are partial-loop injection types that allow you
to inject variable amounts of sample.
Full-loop Injection Type

Use the full-loop injection type when you need the highest possible injection-to-injection
precision and you have sufficient sample to overfill the sample loop. During a full-loop
injection, the autosampler overfills the sample loop, and the mobile phase from the pump
backflushes the contents of the sample loop onto the LC column.
During a full-loop injection, the autosampler performs these tasks:

1. Picks up the sample vial from the vial position that you specify in the acquisition
sequence, and transports the vial to the injection tower.
2. Pushes the sample needle through the vial septum to the depth specified in the method
(Needle Height from Bottom parameter).
Figure 4 shows the autosampler needle descending to a depth of 2 mm from the bottom
of the sample vial.
Figure 4. Needle height from bottom (of the vial)
Flush solvent
Sample
2 mm

1 Introduction
3. Switches the injection valve to the fill position.

4. Withdraws sample solution from the vial and overfills the sample loop.
The speed at which the autosampler withdraws sample depends on the sample viscosity
that you specify in the instrument method (Normal, Medium, or High). The amount of
sample withdrawn depends on the injection volume that you specify in the acquisition
sequence.
The autosampler uses the following algorithm to overfill the sample loop:
Volume withdrawn = Requested injection volume × 1.33 + 70 μL
5. Switches the injection valve to the inject position, allowing the mobile phase to backflush
the sample out of the loop and through the LC column.
6. Flushes the needle tubing and needle with flush solvent from the flush bottle. You specify
the flush volume in the instrument method. The default flush volume is 400 μL.
Pull-loop Injection Type

Use the pull-loop injection type when you have a limited amount of sample. During a
pull-loop injection, the autosampler pulls only the requested sample volume into the sample
loop.
Because dissolved gases can outgas as the autosampler pulls the sample through the needle
tubing, the pull-loop injection type is less precise than the Pushloop injection type. The
bubble formation within the sample slug decreases the reproducibility of the sample volume
pulled into the sample loop.
During a pull-loop injection, the autosampler performs the following tasks:

1. Draws an air bubble into the needle to isolate the incoming sample slug from the flush
solvent already present in the lines.
2. Switches the injection valve to the fill position.
3. Lowers the needle into the sample vial.
4. Draws sample into the needle tubing.
5. Raises the needle out of the vial.
6. Draws air into the needle tubing as it pulls the sample solution into the sample loop.
7. Switches the injection valve to the inject position, allowing the mobile phase from the LC
pump to backflush the sample from the sample loop onto the LC column.

1 Introduction
PushLoop Injection Type

Use the PushLoop injection type when you want to vary the injection volume and
injection-to-injection precision is important.
During a PushLoop injection, the autosampler performs these tasks:

1. Draws sample into the needle tubing and through the injection valve as shown in
Figure 5:
a. Switches the injection valve to the inject position.
b. Draws an air bubble into the needle.
c. Lowers the needle into the sample vial.
d. Draws sample into the needle tubing.
e. Draws a portion of the sample solution through the injection valve.
This step flushes the solvent path between the needle tubing and the sample loop
with the sample solution.
Figure 5. PushLoop injection—step 1
The syringe valve is in
Flush tubing the needle position.
Needle
The sample slug KEY

2
enters the injection 1
valve through port 2 3 From Sample
and exits through 6 pump Mobile phase
port 3. 4 Flush solvent
5
To
column
The mobile phase enters the

injection valve through port 6
and exits through port 5.

1 Introduction
2. Loads the sample loop with the requested injection volume as follows (see Figure 6):
a. Switches the injection valve to the fill position.
b. Pushes the requested injection volume into the sample loop.
Sample loaded
into the loop
2 KEY
1
3 Sample
6 Mobile phase
4 Flush solvent
5
3. Switches the injection valve to the inject position. Mobile phase enters the injection valve
through port 6, backflushing the sample out of the loop and onto the column
(see Figure 7).

1 Introduction
2 From KEY
1
the pump Sample
3
6 Mobile phase
4 Flush solvent
5 To
the column
Operation Modes
The SpectraSYSTEM autosampler has two modes of operation: Stand Alone and SpectraNet.
In the Stand Alone mode, you control the autosampler from its keypad controls and acquire
data to an external device, such as an integrator. In the SpectraNet mode, the SN4000 system
controller controls the SpectraSYSTEM HPLC modules through SpectraNET™
communication. The SN4000 system controller transmits information from the system
modules, such as the autosampler’s tray and column oven compartment temperatures, the
system pressure monitored by the pump, and the data stream from the detector to the data
system computer.
For information on setting up the system for SpectraNET control, see “SpectraNet Mode” on
page 31. For information on controlling the autosampler from the data system, refer to the
Help and manuals provided with the data system.
For information on setting up the system for stand-alone control, see “Stand Alone Mode” on
page 39. For information on controlling the autosampler from its command center, see
“Standalone Operation from the Command Center” on page 63.

1 Introduction
Manual Conventions
Manual Conventions
This manual uses several conventions for working with the autosampler keys and menu
displays.
Autosampler Displays
The autosampler provides a two-line display as shown in the next figure. For manual
illustrations of the autosampler menu, the triangular cursor location is indicated by a caret (>).
• A two-line menu display
>FILES QUEUE TESTS
COMMANDS OPTIONS
Frequently, the two lines shown on the display are only part of a longer menu that you
can see when you press the instrument’s DOWN ARROW key ( ).
In this manual, menus having more than two lines are represented with dashed lines.
• A menu longer than two lines
Configurations 1
Ready Participation
---------------------------------------------------------
Input Polarity
Output Polarity
---------------------------------------------------------
2
Shutdown
Maintenance Log
Text Conventions
This manual uses typographic conventions to differentiate among keys, menus, and fields.
Keys
The manual indicates text keys on the autosampler in all-capital letters, with the exception of
the Samples key. For example: Press the MENU key.
Menus
Use of bold text and the right-arrow key, Menu name > Menu command, indicate instrument
display menu selections. For example: From the main menu, select Files > Load.
Fields
To indicate field names as shown on the instrument display, this manual uses capitalization.
Generally, the first letters of field names are capitalized. For example, in the Samples menu, go
to the Injection Volume field.

1 Introduction
Manual Conventions
Standard Words
For this manual, the words select and enter specifically refer to the autosampler menu
commands and value fields.
Select
The word select is used when you must choose from among available options. For example, to
select a particular menu option, you move the cursor to the appropriate selection and press the
ENTER key. To select a field entry, move the cursor to the appropriate field, and then press
the [+] and [–] keys to scroll to the desired value.
Enter
The word enter is used when you must specify individual alphanumeric digits. To enter a
particular value, move the cursor to the field and press the [+] and [–] keys to increment or
decrement each digit in the field until the desired value or letter appears.

1 Introduction
Specifications
Specifications
These are the specifications for the SpectraSYSTEM AS3000 autosampler.
Vial capacity: 105 in three removable trays

Note For earlier versions of the autosampler, the tray temperature control unit was a
hardware option. The tray compartment for autosamplers that do not have this
option installed hold 120 vials in three removable trays.
Variable-volume:
Injection precision <0.5% RSD @ 10 μL or greater
Injection volume • 0.1 to 100 μL injection standard (250 μL syringe)
• Up to 1000 μL injections with larger loops and syringes
Fixed-loop:
Injection precision <0.5% RSD @ 10 μL or greater
Injection volume • 20 μL standard (250 μL syringe)
• 1000 μL injections with larger loops and syringes
Sample carryover: Typically <0.01% at 400 μL flush volume
Note The flush volume is user-settable from 0 to 5000 μL.
Minimum sample volume: 1 μL can be injected from a sample volume of 10 μL with a standard needle
Needle height: Settable in 0.1 mm increments from 0 to 20 mm
Column oven (optional): • Settable in 1° increments from 20 to 80 °C, starting at 5 °C above ambient
• Temperature stability typically ±0.2 °C
• Accommodates up to 30 cm columns
Method files: • Protected in non-volatile memory
Communications: • Pump Ready
• Inject Hold
Outputs: • Pump Stop
• Autosampler Ready
• Inject
• Gradient Start
• Four timed-event outputs
• BCD (optional)
• SpectraNET/RS-232 port
Dimensions: 14.5 in. (37 cm) × 17 in. (43 cm) × 20 in. (51 cm) (h×w×d)
Weight: 53 lb. (24 kg) with temperature-controlled tray and column oven compartments
Power requirements: 100/120 VAC, 220/240VAC, 50/60 Hz, 450VA
Environmental: 10 to 40 °C; 5 to 95% relative humidity, noncondensing
Safety/EMC compliance: CSA, TÜV, UL, FCC, CE Mark, EMC and Low Voltage Directives

2
Installation
This chapter describes the site requirements, installation procedures, and performance testing
for the Thermo Scientific SpectraSYSTEM AS3000 autosampler.
Before you unpack the autosampler, read the instructions on lifting the autosampler (see
“Lifting the Autosampler” on page 17).
The following items are factory installed: a 250 μL syringe, three sample trays, a sample
needle, and a 100 μL sample loop.
Contents
• Startup Checklist
• Site Requirements
• Lifting the Autosampler
• Unpacking the Autosampler
• Connecting the Autosampler to the Building Ground
• Connecting the Plumbing
• Installing the Column Compartment Cover
• Installing the Sample Trays
• Powering-Up the Autosampler
• Priming the Autosampler
• Communication: SpectraNet or Stand Alone
• Performance Verification

2 Installation
Startup Checklist
Startup Checklist
This list summarizes the tasks that are required to install your autosampler. Complete
installation information is contained in this chapter.
To install the autosampler, use these tools:

• Phillips screwdriver (1)
• 1/4 in. open-end wrench (2)
• Small, standard screwdriver (1)
Unpacking
U Unpack and inspect your instrument. “Unpacking the Autosampler” on page 18
U Remove cardboard/foam packing insert from the sample
compartment (tub).
U Check for parts shortages.
U Read the Safety Information section.
Back panel
U Place the autosampler so that the back panel is accessible. “Site Requirements” on page 16
U Install filter/solvent line and flush bottle.
U Connect the power cord. “Powering-Up the Autosampler” on page 29
U Connect the autosampler to the building ground. “Connecting the Autosampler to the Building
Ground” on page 19
U Hardwire the external events terminals and make the
connections to other SpectraSYSTEM instruments.
U For an autosampler under SpectraNET control, make the “Connecting the System Synchronization
hardwire connections to other SpectraSYSTEM instruments Harness” on page 37 and
and connect the instruments to the SN4000 system “Connecting the SpectraSYSTEM Devices to the
controller. SN4000 Controller” on page 31

2 Installation
Startup Checklist
Front panel
U Install the solvent tray/waste container. “Installing the Solvent Waste Container” on
page 22
U Connect the autosampler to the pump: “Connecting the Pump to the Autosampler” on
page 24
On instruments with the column oven installed, connect the
pump outlet line to the solvent preheat tube.
U Mount the LC column: “Installing the Column” on page 25
On instruments with the column oven installed, install the

column between the column mounts, secure the column
mounts to the oven, and connect the inlet end to injection
valve port 5.
U Connect the autosampler to the detector. “Connecting the LC Column’s Outlet to the
(Connect 12 in., 0.010 in. ID tubing to the inlet side of Detector’s Flowcell Inlet” on page 26
flowcell.)
Startup/priming
U Turn on the autosampler and check the initial response to “Powering-Up the Autosampler” on page 29
power-on.
U Using the 250 μL syringe, flush the lines with 500 μL of
solvent.
Performance verification
U Run a standard sample (a test mix is shipped with the “Performance Verification” on page 49
instrument).
U Date and retain run results with instrument documentation.
U Customize the READY participation settings. “Ready Participation” on page 48
U Run an unretained sample to determine the system gradient “Gradient Delay” on page 99
delay time.
U Optimize the needle height. The default value of 2 mm is “Needle Height” on page 95
appropriate for most applications.
Installed by:
(Name) (Date)

2 Installation
Site Requirements
Site Requirements
These topics describe the space and electrical requirements for the SpectraSYSTEM
autosampler:
• “Space” on this page
• “Electrical” on page 17
Space
The autosampler weighs 24 kg (53 lbs) and requires a team effort to lift. Before you lift the
autosampler, read the lifting instructions in “Lifting the Autosampler” on page 17. The
instrument requires a bench space at least 14.5 in. (37 cm) × 17 in. (43 cm) × 20 in. (51 cm)
(h×w×d). Be sure to allow adequate ventilation away from heating or air conditioning ducts.
Avoid exposing the autosampler to direct sunlight. If used with the SpectraSYSTEM pump
and detector, place the autosampler in the middle (see Figure 8).
Tip You might want to set your instrument on the benchtop so that you have easy access
to the back panel.
Figure 8 does not show the vacuum membrane degasser. Place the vacuum membrane
degasser to the left of the LC pump.
Figure 8. SpectraSYSTEM LC system benchtop setup
LC Pump Autosampler Detector
CAUTION If you use hazardous solvents, be sure to use the proper venting apparatus.

2 Installation
Lifting the Autosampler
Electrical
Your autosampler automatically configures itself to operate from the local line voltage
(100 to 260 VAC at 50 or 60 Hz). You do not need to set the line voltage. The instrument
arrives with the necessary fuses installed.
To avoid intermittent failures and unexplained occurrences (lockup, loss of memory, incorrect
operation) that are directly related to poor power, provide a stable, spike-free power source.
Thermo Fisher Scientific recommends the use an uninterruptible power supply (UPS) for
maximum protection from power-related failures.
CAUTION The UPS unit must meet the appropriate safety standards and be certified by
authorized agencies for your country (Authorized agencies include TÜV, CSA, UL, and so
on. The CE mark is accepted in most countries.) Thermo Fisher Scientific cannot
guarantee that the LC system meets the appropriate safety standards when you connect
uncertified devices to the autosampler.
Lifting the Autosampler

The autosampler, at 24 kg (53 lbs) and a height, width, and depth of 37 × 43 × 51 cm
(14.5 × 17 × 20 in.), is too heavy and too bulky for one person alone to lift safely. In addition,
any jarring or uneven movement can cause misalignment of the autosampler’s XYZ arm.
In accordance with international safety regulations, lifting the autosampler requires a team
effort. Moving the autosampler from one benchtop to another requires two people to
simultaneously lift the autosampler onto a movable cart. Using the lift points underneath the
left and right sides of the autosampler, have one person lift the left side of the autosampler
while the second person lifts the right side of the autosampler.
Figure 9 shows the lift point underneath the right side of the autosampler.

2 Installation
Unpacking the Autosampler
Figure 9. Lift point on the right side of the autosampler
Unpacking the Autosampler

Your autosampler arrives in a specially designed shipping container to protect it from damage
during transit. When it arrives, inspect all containers and immediately report any damage in
transit to the transportation company. Have the carrier note the shipping crate's condition on
both the delivery receipt and the freight bill. The carrier is responsible for all damage incurred
in shipment.
The SpectraSYSTEM autosampler arrives with the sample trays and syringe installed. A
cardboard shipping insert on top of the sample trays restrains the XYZ arm and holds the
sample trays in place during shipment. Remove the shipping insert. Retain both the shipping
insert and shipping crate should future shipment become necessary.
After unpacking, inspect your autosampler and its accessories for missing parts, physical
damage, or both. If you find damage, notify both the carrier and your Thermo Fisher
Scientific representative. You must obtain authorization from Thermo Fisher Scientific prior
to returning any goods.

2 Installation
Connecting the Autosampler to the Building Ground
The shipping kit contains the following:

• Autosampler
• Accessory Kit (See Chapter 8, “Replaceable Parts.”)
• Vial Kit (See Chapter 8, “Replaceable Parts.”)
• Declaration of Conformity
• SpectraSYSTEM documentation CD (contains the user guides for the SpectraSYSTEM
family of LC products)
The accessory kit contains three sample trays and the vial kit contains a supply of vials,
silicone and Teflon™ septa, and screw-top vial caps. You can order additional vials from
Thermo Fisher Scientific. To ensure smooth autosampler operation, use standard size vials.
For information about installing the sample trays in the autosampler tray compartment
(sample tub), see “Installing the Sample Trays” on page 27.

Before you turn on the autosampler, connect the grounding post on the back of the
autosampler to the building ground.
CAUTION To avoid electric shock, make sure that the autosampler is connected to
ground. Connect the power cord to a power outlet with a protective earth ground (see
“Powering-Up the Autosampler” on page 29). Connect the grounding post on the back of
the autosampler to the building ground.
Y To connect the autosampler to the building ground
1. Connect one end of a conductive wire to the grounding post on the back of the
autosampler (see Figure 10).
2. Connect the other end of the conductive wire to the building ground, for example, to an
exposed metal fixture such as the building's water pipe.

2 Installation
Figure 10. Autosampler grounding post connected to ground

Grounding post
Conductive wire
connected to the
building ground
12
11
10
9
8
7
6
5
4
3
2
WARNING 1
Earth Connection Essential

Before Connecting Supply!
C
O
M
M
ATTENTION
Raccordement a la terre
indispensable avant
le raccordement a l’alimentation!
WARNUNG
Vor Dem Anschluss des Netzteils
Unbedingt Erdung TERMINAL CONFIGURATION
des Gerates Vornehmen! AS 3000 12.
11.
Description
TIMED EVENT 1
TIMED EVENT 2
Signal
OUT
OUT
10. TIMED EVENT 3 OUT
SPECTRA AutoSampler 9.
8.
TIMED EVENT 4
A/S READY
OUT
OUT
OVEN-TEMP/COOLER 7.
6.
INJ HOLD
INJ OUT
IN
OUT
5. PUMP READY IN
4. GRAD START OUT
3. PUMP STOP OUT
2. + 5V 150mA OUT
1. GROUND ----
This product is manufactured under, and covered by, one or more of the following U.S. patents:
4,478.095 4,957,009 5,044,428
4,953,075 5,029,065
355 River Oaks Parkway

San Jose, CA 95134 U.S.A.
Serial No: 180000

Assembled in China
Model No: AS 3000
This device complies with FCC Rules, Part 15.

Operation is subject to the following two conditions:
61010 - 1
(1) This device may not cause harmful interference,
and (2) This device must accept any interference
received, including interference that may cause
undesired operation.
CAUTION
SERVICE BY QUALIFIED PERSONNEL ONLY.
NO USER SERVICEABLE PARTS INSIDE.
FOR CONTINUED PROTECTION AGAINST FIRE HAZARD,

REPLACE FUSE ONLY WITH SAME TYPE AND RATING.
LINE 100 V 120 V 220 V 240 V 50/60 HZ

FUSE T5.0 A T2.5 A 450 VA

2 Installation
Connecting the Plumbing

To install the solvent bottles and connect the plumbing, follow these procedures:
• “Connecting the Flush Solvent Bottle” on this page
• “Installing the Solvent Waste Container” on page 22
• “Connecting the Pump to the Autosampler” on page 24
• “Installing the Column” on page 25
• “Connecting the LC Column’s Outlet to the Detector’s Flowcell Inlet” on page 26
Connecting the Flush Solvent Bottle

Your accessory kit includes a 250 μL flush-solvent bottle and cap. The cap assembly comes
with the 1/8 in. OD × 1/16 in. ID Teflon inlet line and high-molecular-weight polyethylene
filter attached.
Note If you want to use your own solvent bottle or another container, be sure that it is
clean and chemically inert. For best results, use glass bottles.
Y To install the flush bottle
1. Rinse the bottle with LC-grade solvent to remove any dust. Fill the bottle with the
appropriate LC-grade solvent.
2. Insert the filter into the solvent bottle and screw on the cap. Make sure that the inlet filter
rests on the bottom of the solvent bottle.
3. Connect the free end of the Teflon inlet line to the flush line on the back of the
autosampler (see Figure 11).

2 Installation
Figure 11. Autosampler back panel connections
12
11
10
9
8
Factory-installed
7
6
5
4
flush line with union
3
2
WARNING 1

C
O
ATTENTION
M
M
COMM port
indispensable avant
WARNUNG
11.
Description
TIMED EVENT 1
TIMED EVENT 2
Signal
OUT
OUT
8.
TIMED EVENT 4
A/S READY
OUT
OUT
OVEN-TEMP/COOLER 7.
6.
INJ HOLD
INJ OUT
IN
OUT
5. PUMP READY IN
4. GRAD START OUT
3. PUMP STOP OUT
2. + 5V 150mA OUT
1. GROUND ----
4,478.095 4,957,009 5,044,428
4,953,075 5,029,065

Serial No: 180000

Assembled in China
Model No: AS 3000

61010 - 1
CAUTION

LINE 100 V 120 V 220 V 240 V 50/60 HZ

Fuse compartment
AC power
CAUTION Many LC solvents are hazardous. Make sure to handle them properly and
dispose of any waste solvents in an environmentally correct manner.
4. Place the flush bottle in a secondary container.
Installing the Solvent Waste Container

The solvent waste container (the flat, white plastic container included in your accessory kit)
can hold 100 mL of waste. To install it, slide it into the compartment under the front left side
of the instrument.
Note The general caution label on the left side of the autosampler below the column oven
compartment is a reminder to empty the solvent waste container. The default flush
volume for an injection cycle is 400 μL. This means that you can overfill the solvent waste
container within 250 injections.
Note The back of the compartment prevents the tray from sliding too far under the
instrument.

2 Installation
Orient the tray so that the black plastic, barbed elbow fitting is directed through the hole in
the liquid collection trough (across the front of the instrument) as shown in Figure 12.
Figure 12. Autosampler front panel connections
2×24
alpha-numeric
display RUN STATUS MENU
STOP
ENTER
Samples AS3000
Single-piece
injection
needle
To flush valve
Oven
(optional)
WA R N IN G
From pump
Elbow fitting
Liquid collection Solvent Solvent pre-heat Aluminum mounting plates Power To detector
trough waste tube (oven models only) switch
container
Note Sometimes the barbed elbow fitting becomes dislodged during shipping. Be sure
that the end of the barbed fitting is directed through the hole (not into the trough).
For larger injection applications, or for those requiring frequent flushing, you might want to
install a piece of Tygon™ tubing onto the waste port to allow the waste to flow to a carboy or
other large container for waste collection.
To hook up your waste container, locate the Tygon tubing included in your accessory kit and
connect it to the end of the black, barbed fitting. To prevent backflushing into the lines, place
the container lower than the instrument. Direct the Tygon tube into your container.

2 Installation
Connecting the Pump to the Autosampler

Note Your standard accessory kit contains two pieces of 0.010 in. ID stainless-steel tubing
(one 4 in. piece and one 12 in. piece). The 12 in. piece is included to make the
column-detector connection if the detector is not a SpectraSYSTEM detector. If you are
connecting the pump to a SpectraSYSTEM detector, you can use the 12 inch tubing to
make the pump-autosampler connection.
The autosampler arrives with the column oven assembly and the flush and needle lines already
installed. The stainless-steel, low dead-volume union that connects the pump outlet tubing to
the column oven tubing is also factory installed. You have to connect the pump to the zero
dead-volume union (ZDV). The preheat line runs behind the column oven, through the
oven's mantle, up through the service loop, and into the injection valve. For standard
analytical configurations, this line holds approximately 180 μL of preheated solvent.
Instruments with 0.007 in. narrow-bore preheat tubing provide approximately 22.7 μL of
preheated solvent.
Y To connect the pump to the preheat tube
1. Remove the column oven cover (if you have not already done so) and set it aside.
Tip The cover fits snugly. To remove it, place your fingers or thumb in the
indentation on the top edge of the column door and firmly pull it back toward you.
2. Route your pump outlet line through the lower notch on the left side of the autosampler.
3. Connect the line to the low dead-volume union on the preheat tube as follows:
a. Locate the ferrule included in your accessory kit.
b. Thread the tubing through the fitting, and place the ferrule on the end of the preheat
tube.
c. Use two 1/4 inch wrenches to tighten the connection. Use one wrench to hold the
union body and one to tighten the nut 1/8-turn past the stop.
Figure 13 shows the connection between the LC pump outlet and the preheat tube inlet.

2 Installation
Figure 13. LC pump outlet-to-preheat tube inlet connection
RUN STATUS MENU
STOP
ENTER
SAMPLES SpectraSYSTEM AS3000
WARNING
Low dead-volume
Pump outlet line Nut Ferrule union
Installing the Column

The LC column is placed between two aluminum column mounts that attach to the column
oven's plate. The aluminum mounts improve the heat transfer from oven to column.
The LC column secures directly onto the front of the oven plate. The instrument arrives with
the column mounts already installed.
Y To mount the LC column
Tip To ensure that no air gets into the column, remove air from the solvent lines
before connecting the column.
1. Use a flat blade screwdriver to loosen the mounting screws and to remove and separate the
column mounts.
Tip Thermo Scientific columns are usually connected so that liquids flow from left to
right as you read the label. If you are not using a Thermo Scientific column, refer to
your column documentation to orient it in the correct direction of flow.
2. Place the column between the column mounts, and replace the mounting screws to secure
the column in place.

2 Installation
Connecting the LC Column’s Outlet to the Detector’s Flowcell Inlet

The accessory kit includes a 12 in. length of 0.010 in. ID tubing that you can use to connect
the LC column outlet to a non-SpectraSYSTEM detector’s flowcell inlet. The flowcell of a
SpectraSYSTEM detector has an inlet line of sufficient length to reach the LC column outlet.
Y To connect the LC column’s outlet to the detector’s flowcell inlet
1. Depending on the detector, do one the following:

• For a SpectraSYSTEM detector, using the appropriate high-pressure fittings, connect
the flowcell’s inlet line to the outlet of the LC column (see Figure 14).
• For a non-SpectraSYSTEM detector, using the appropriate high-pressure fittings,
connect one end of the 12 in. length of 0.010 in. ID tubing (found in the accessory
kit) to the column outlet and the other end to the flowcell inlet.
2. Replace the column oven cover, snapping it firmly into place (see “Installing the Column
Compartment Cover” on page 27).
Figure 14. LC column outlet-to-flowcell inlet connection
RUN STATUS MENU

RUN STATUS MENU
STOP
STOP
ENTER
ENTER
SAMPLES SpectraSYSTEM AS3000 ZERO SpectraSYSTEM UV2000
WARNING
Connection between
the LC column
and the flowcell inlet

2 Installation
Installing the Column Compartment Cover
Installing the Column Compartment Cover

Y To install the column compartment cover
1. Insert the tabs on the bottom of the cover into the front lower edge of the autosampler.
2. Route the solvent lines through the slots on the sides of the column compartment.
3. Snap the top of the cover in place.
Installing the Sample Trays

Your autosampler comes with three sample trays and a supply of vials, silicone and Teflon
septa, and screw-top vial caps. You can order additional vials from Thermo Fisher Scientific.
To ensure smooth autosampler operation, use standard size vials.
IMPORTANT Be sure to use a 40 to 60 mil (1.0 to 1.5 mm) rubber or silicone septum
with a 5 mil (0.1 mm) Teflon liner on one side.
Each tray contains 35 vials arranged in seven rows of five (see Figure 15).
Figure 15. 35-vial autosampler tray
Vial position 1
Vial position 35
Trays A, B, and C are arranged in the autosampler from left to right. The first tray and vial
position is A01; the last is C35.
IMPORTANT Be sure to use a 40 to 60 mil (1.0 to 1.5 mm) rubber or silicone septum
with a 5 mil (0.1 mm) Teflon liner on one side.

2 Installation
Installing the Sample Trays
Y To install the sample trays
1. Hold the tray handle, tilting the back end down (see Figure 16).
Figure 16. Installing a sample vial tray
Sample tray handle

(front) Tray positions
A
B
C
Slots
Tub Runner
2. Insert the tray's runners into the slots in position A at the back of the tub.
3. Lower the front of the tray into place and press down firmly to seat the tray.
Tip Pull the handle back toward you until the tray snaps into place. Try moving each
tray from side to side to be sure that it is seated completely.
4. Insert the other two sample trays into positions B and C.
IMPORTANT Be sure that each tray is properly seated. Each tray's upper front edge
should fit under the upper lip of the tub. If a tray is not completely seated, the
autosampler does not correctly pick up or return vials to that sample tray.

2 Installation
Powering-Up the Autosampler
Powering-Up the Autosampler

Your autosampler arrives with the correct fuses installed.
CAUTION Before you turn on the power switch, ensure that the autosampler is connected
to the building ground (see “Connecting the Autosampler to the Building Ground” on
page 19).
Y To connect the autosampler to line power and power-up the autosampler
1. Locate the power cord in the shipping container (not in your accessory kit).
2. Insert one end into the AC power receptacle on the back panel and the other end to a
grounded power outlet.
3. Turn on your instrument by pressing the on/off button on the lower right corner just
below the front panel (see Figure 14 on page 26).
During startup, the instrument's self-diagnostic goes through the following sequence:
1. Completes a series of ROM checks.
2. Completes a series of RAM checks.
3. Activates the injection valve.
4. Verifies the proper connections on all installed options.
5. Verifies the proper operation of all sensors.
6. Homes (returns to starting position) all syringes and motors.
Priming the Autosampler

After you have completed the plumbing and power-up procedures and started your
instrument, you must prime your autosampler to wet all of the lines. To do so, flush all
syringes and lines with an appropriate solvent.
IMPORTANT The autosampler is shipped with methanol in the lines. Be sure to use a
miscible solvent.
For complete instructions on using the autosampler keypad controls, see “Keypad Controls”
on page 57.

2 Installation
Communication: SpectraNet or Stand Alone
Y To prime the autosampler
1. If you have not already done so, fill your flush solvent bottle.
2. Press the MENU key and select COMMANDS.
The Commands menu appears (see Figure 17).
Figure 17. Commands menu
3. Select Flush Sample Syringe to access the menu shown in Figure 18.
4. Press the [+] and [–] keys to select 5000 μL. Then press the ENTER key to initiate the
flush operation.
Figure 18. Flush Sample Syringe menu
The autosampler flushes the sample syringe and flush lines with the specified volume of flush
solvent and returns the syringe to its starting position. The recommended 5000 μL flush takes
approximately ten minutes. During the flush sequence, a confirmation message is displayed.

You can configure the SpectraSYSTEM autosampler to send information to other Thermo
Scientific SpectraSYSTEM modules or to non-SpectraSYSTEM LC instruments, as follows:
• SpectraNet mode: Use the SpectraNet mode as a part of a SpectraSYSTEM
chromatograph connected to other SpectraSYSTEM modules through the SN4000
system controller, and controlled by your chromatography data system.
• Stand Alone mode: Use the Stand Alone mode if you hardwired the autosampler to other
non-SpectraSYSTEM HPLC modules through the remote input and output connectors,
or connected it to older SpectraSYSTEM and non-SpectraSYSTEM instruments by
means of specialized cables, communication protocols, or both.
This section contains the following topics:

• SpectraNet Mode
• Stand Alone Mode
• Stand-Alone Communication to Integrators
For complete instructions on using the autosampler keypad controls, see “Keypad Controls”
on page 57.

2 Installation
SpectraNet Mode
Configured as a SpectraSYSTEM module using SpectraNET communication and the
SN4000 system controller, your autosampler is automatically controlled by your
chromatography data system. The chromatography data system assumes almost all keyboard
control and coordinates the majority of the autosampler's operations.
To set up the SpectraSYSTEM modules to communicate with the data system computer
through the SN4000 controller, follow these procedures:
• “Connecting the SpectraSYSTEM Devices to the SN4000 Controller” on this page
• “Connecting the SN4000 Controller to the Data System Computer” on page 34
• “Setting the Configuration to the SpectraNet Mode” on page 35
To synchronize the input and output signals during a run, follow these procedures:
• “Setting Up the Autosampler and Pump Contact Closure Signals” on page 36
• “Connecting the System Synchronization Harness” on page 37
Connecting the SpectraSYSTEM Devices to the SN4000 Controller

Use RJ11 cables to connect a SpectraSYSTEM UV/VIS or fluorescence detector, a
SpectraSYSTEM pump, and a SpectraSYSTEM autosampler to the SN4000 controller. Use
an RJ45 cable and an RJ45 to DB9 adapter to connect the SN4000 controller to the data
system computer.
Y To connect the communication cables to the SN4000 controller
1. Turn the SN4000 power switch to the Off position, and then disconnect the 12 V dc
power supply
Figure 19 shows the power switch and the Power In port on the back panel of the
SN4000 controller.
Figure 19. SN4000 controller back panel
ON
Power
I
switch
O
RESET
Power In
port
POWER IN
12VDC

2 Installation
CAUTION Before you remove the top cover of the SN4000 controller, turn the power
switch on the back of the controller to the Off position, and then disconnect the 12 V dc
power supply.
2. Remove the top cover of the SN4000 controller as follows:

a. Turn the SN4000 controller upside down to access the four screws that secure the top
cover to the case (see Figure 20).
Figure 20. Screws that secure the top cover to the case (bottom view of the controller)
Two screws
Two screws
b. Using a #2 Phillips head screwdriver, remove the screws and slide the top cover off the
case.
Figure 21 shows the SN4000 PCB.

2 Installation
Figure 21. SN4000 PCB
U12 socket
U11 U29
U12 U28
HOST COM SPARE DET 2 INT DET 1 A/S PUMP
RJ11 ports
(for the detector, autosampler,
RJ45 port and pump connections)
(for the data system
computer connection)
3. Verify that the EPROM firmware version 9.05 (P/N A4636-129) is installed in socket
U12 on the SN4000 PCB and that sockets U11, U28, and U29 are empty.
4. To connect a SpectraSYSTEM pump to the SN4000 controller, do the following:
a. Connect one end of an RJ11 6-pin, 4-wire cable to the PUMP port on the SN4000
PCB.
b. Route the cable through the access hole on the back panel of the controller.
c. Connect the other end of the cable to the COMM port on the back panel of the
pump.
5. To connect a SpectraSYSTEM autosampler to the SN4000 controller, do the following:
a. Connect one end of an RJ11 6-pin, 4-wire cable to the A/S port on the SN4000
PCB.
b. Route the cable through the access hole on the back panel of the controller.
autosampler.

2 Installation
6. To connect a SpectraSYSTEM UV/Vis or fluorescence detector to the controller, do the

following:
a. Connect one end of an RJ11 6-pin, 4-wire cable to the DET 1 port on the SN4000
PCB.
b. Route the cable through the access hole on the back panel of the SN4000 controller.
UV/Vis or fluorescence detector.
Connecting the SN4000 Controller to the Data System Computer
Y To connect the SN4000 controller to the data system computer
1. Connect one end of an RJ45 8-pin, 8-wire cable to the Com port on the SN4000 PCB.
2. Route the cable through the access hole on the back panel of the SN4000 controller.
3. Connect an RJ45 to DB9 adapter to the other end of the cable (see Figure 22).
Figure 22. RJ45 to DB9 adapter
RJ45RJ-45
to DB9toadapter
DB9
Adapter
1 8
RJ45 88-Pin
RJ-45 pin
RJ45 cable jack

RS232
Serial Communication
4. Connect the DB9 adapter to one of the RS-232 ports on the back panel of the data
system computer.
5. Reinstall the SN4000 controller top cover. Using a #2 Phillips screwdriver, tighten the
screws that secure the cover to the case.
6. Reconnect the power cable from the 12 V dc power supply to the Power In inlet on the
back panel of the SN4000 controller.

2 Installation
Setting the Configuration to the SpectraNet Mode

To control the SpectraSYSTEM LC system from a data system computer, the
SpectraSYSTEM autosampler must be set to the SpectraNet communication mode.
Y To configure your autosampler to use SpectraNet communication
1. Turn on your autosampler, wait for the power-up sequence to complete, and then press
the MENU key.
The main menu appears (see Figure 39 on page 61).
2. Select OPTIONS > Configurations.
The Configurations menu appears (see Figure 23).
Figure 23. Configurations menu in SpectraNet mode
Sample Syringe 250
Prep Installed No
---------------------------------------------------------
Oven Installed Yes
TrayTemp Installed No
Key Repeat Rate Medium
File Name Protect
1: Off
2: Off
3: Off
4: Off
Mode SpectraNet
Solv Viscosity Normal
3. Move the cursor to the Mode field, and press the [+] and [–] keys to select SpectraNET.
Then press ENTER to accept the field value and exit the Configurations menu.

2 Installation
Setting Up the Autosampler and Pump Contact Closure Signals

Before you can control the run timing of the SpectraSYSTEM modules from a data system
computer, you must configure the polarity of the contact closure signals for both the
autosampler and the pump.
Y To set up the autosampler’s contact closure signals
1. On the autosampler keypad, press the MENU key.

2. Press the LEFT ARROW ( ) or RIGHT ARROW ( ) key to select OPTIONS, and
then press the ENTER key.
3. Press the DOWN ARROW ( ) key to select Input Polarity, and then press the ENTER
key.
The Input Polarity screen appears with Pump Ready Active selected (see Figure 24).
Figure 24. Input Polarity screen
Pump Ready Active Hi

Inj Hold Active Lo
4. Use the [+] and the [−] keys to select Hi.

5. Press ENTER to accept the field value and exit the Configurations menu.
Y To set up the pump’s contact closure signals
1. On the pump keypad, press the MENU key.

2. Press the LEFT ARROW ( ) or RIGHT ARROW ( ) key to select OPTIONS, and
then press the ENTER key.
3. Press the LEFT ARROW ( ) or RIGHT ARROW ( ) key to select More, and then
press the ENTER key.
The More menu for the pump appears.
Figure 25. More menu for the SpectraSYSTEM pump
Pressure Units PSI
Purge Mode Flow
Delay Volume 0.0

Cursor Speed Medium
Status Lock Off

Ready Output Active Hi

2 Installation
4. Press the DOWN ARROW ( ) key to select Ready Output Active, and then press the
ENTER key.
5. Press the [+] and the [−] keys to select Hi.
6. Press the ENTER key to accept the value and exit the More menu.
Connecting the System Synchronization Harness

The timing of the SpectraSYSTEM modules is synchronized through a contact closure wiring
harness (see Figure 26). The harness has one connector each for the pump, detector, and
autosampler.
Figure 26. Contact closure wiring harness for the SpectraSYSTEM LC system
8
7
6
5
4
PUMP
3
2 12
1 11
10
9
8
DET 7
DATE CODE 6
S/N 12
P/N A5596 REV 11 5
10 4
9 3
8 2
A/S 1
7
6
5
4
3
2
1
Y To connect the system synchronization harness
1. Connect the cable labeled PUMP to the 8-pin terminal on the back panel of the
SpectraSYSTEM pump (see Figure 27).
2. Connect the cable labeled AS to the 12-pin terminal on the back panel of the
SpectraSYSTEM autosampler (see Figure 27).
3. Connect the cable labeled DET to the 12=pin terminal on the back panel of the detector
(see Figure 27).
Note For information on connecting the SpectraSYSTEM UV8000 Vacuum Degasser

and PDA Detector module to the LC pump and autosampler, refer to the SpectraSYSTEM
UV8000 Vacuum Degasser and PDA Detector Hardware Manual.

2 Installation
Figure 27. Contact closure connections for a typical SpectraSYSTEM LC system
Pump
C
Autosampler O
M
M
12
11
10
UV2000 Detector 9 8 Green
8 7 White
COMM 1211 10 9 8 7 6 5 4 3 2 1 7 Green 6
6 White 5
5 Black 4
4 Red 3 Blue
3 2 Red
1 Black
2
1 Blue
Black
Clear
Blue
D
E
G
C A
S
PUMP
O
M
M
AS
DET
Contact Closure
Wiring Harness
(P/N A5596-010, Rev E

2 Installation
Stand Alone Mode

Use the Stand Alone mode to operate SpectraSYSTEM modules without data system control.
With the 12-pin terminal on the instrument's back panel, you can hardwire the injection
synchronization signals between your autosampler and other components in an LC system
(see Figure 28).
Figure 28. 12-pin terminal
12
11
10
9
12
11
10
8
7
9
8
7
6
5
4
3
2
1
6
5
C
O
M
M
4
3
2
1
C
O
M
M
TERMINAL CONFIGURATION
AS 3000 T E R MINA
12.
L C ONF IG URSignal
Description
DE STIMED
C R IP T EVENT
ION
11. TIMED EVENT 2
12.
1
AT ION
OUT
S IG NA
OUT
L
10.T IME D E V E NT 1
TIMED
D E V EEVENT
3 OUT
OUT
SPECTRA AutoSampler 11. T IME
9. T IME
10. TIMED
9.8. T IME
A/SD READY
NT 2
D E V EEVENT
4
NT 3
E V E NT 4
OUT
OUT
OUT
OUT
OUT
8.7. A/SINJ
R E ADY OUTIN
OVEN-TEMP/COOLER 7. INJ HOLD
6.6. INJINJ
HOLD
OUTOUT
IN
OUTOUT
5.5. P UMP
PUMP READY
R E ADY IN IN
4.4. G RGRAD
AD S TAR T
START OUTOUT
3. P UMP S T OP OUT
DAT E OF MANUFAC T UR E : 2.3. +5VPUMP
150MASTOP OUTOUT
1.2. G R+OUND
5V 150mA OUT
1. GROUND ----
T HIS P R ODUC T IS C OV E R E D B Y ONE OR MOR E OF T HE F OLLOWING PAT E NT S :
This 4,957,009
product is manufactured under, and covered by, one or more of the following U.S. patents:
4,953,075
4,478.095 4,957,009 5,044,428
4,478,095
4,953,075 5,029,065
Use a combicon connector (found in the accessory kit) to attach control wires from other LC
devices to the 12-pin terminal. Once you have made all the connections, you can make and
break connections without disturbing individual wires.
Y To connect a wire to the combicon connector
1. Loosen the appropriate screw.

2. Insert the wire.
3. Tighten the screw.

2 Installation
With hardwire communications, the autosampler can start and stop a pump or detector, begin
a gradient program (gradient pumps only), or control other features of the externally
connected instruments. In addition, the terminal has four timed-function outputs that you
can use to control valve-switching devices or other devices on a timed basis. To set up a
timed-events program, see “Timed Events Menu” on page 72.
To set up your stand-alone system, follow these topics as appropriate:

• “Input and Output Terminal Specifications” on this page
• “Pin Assignments” on page 41
• “Recommended Hardwire Connections for a Stand-Alone System” on page 42
• “Communications Menu Parameters” on page 43
• “Setting the Polarity of the Autosampler Signals” on page 44
• “Stand-Alone Communication to Integrators” on page 46
• “ChromJet or DataJet Communication” on page 47
• “BCD Communication” on page 47
• “Ready Participation” on page 48
• “Hardware Configurations” on page 49
Input and Output Terminal Specifications

The twelve terminals on the autosampler’s back panel can be divided into two groups: outputs
and inputs.
The output terminals, including Time Functions 1 through 4 (TF1-4), are open-collector
outputs capable of sinking (handling) currents up to 600 mA at voltages up to 24 VDC. The
active state is user programmable in the Timed Events menu (see “Timed Events Menu” on
page 72).
The input terminals accept TTL-level inputs, with a transition activating each. The two
inputs are tied to +5 VDC through pull-up resistors. A "Lo" level is from 0 to 0.8 V; a "Hi"
level is from 2 to 5.5 V.
IMPORTANT All inputs and outputs are referenced to ground.

2 Installation
Pin Assignments
Table 1 list the input and output pin assignments.
Table 1. Input and output pin assignments (Sheet 1 of 2)
Pin # Assignment
Pin 1 Use this pin as the ground reference used for all inputs and outputs.
GROUND:
Pin 2 Use this regulated +5 VDC supply to power pull-up resistors or external relays. The current
+5VDC: is limited to a maximum of 300 mA to protect against external short circuits affecting the
autosampler's operation.
Pin 3 Use this pin to send a pulsed output signal to stop the pump after the last sample has been
PUMP STOP processed. It is activated when the last sample in the queue has completed its last injection,
(output): or when the shutdown file has been activated (using the special shutdown command). For
more information on the Shutdown command, see “Automated Shutdown in the Stand
Alone Mode” on page 123.
Pin 4 Use this pin to send a signal to the pump to start its gradient program. The autosampler
GRADIENT START send this signal at a specified amount of time before it activates the Inject Out pin. The
(output): time is specified as the Gradient Delay value in the More menu (under Files). This
momentarily active, preinjection signal permits the gradient to start prior to sample
injection to compensate for the system delay volume. The result is an injection that occurs
just as the gradient front reaches the injection valve. For more information on the gradient
delay function, see “Gradient Delay.”
Pin 5 Through this input, the pump signals the autosampler that the mobile-phase flow rate is
PUMP READY stable and that the pump is ready for an analysis to begin. (You can connect other devices
(input): here as well.) This input must be continuously active for the autosampler to proceed with
injections. From the Input Polarity menu, you can select whether a high or low level on this
line means "ready." The default is Hi.
Pin 6 Use this output pin to synchronize the timing of external devices (pumps, detectors,
INJECT OUT integrators, and so on) to the autosampler injection. This line sends a momentary signal
(output): each time the autosampler makes an injection. For the specifications of this output, see
“Input and Output Terminal Specifications” on page 40.
Pin 7 Use this input pin to keep the autosampler in the hold state with sample in the loop.
INJECT HOLD Releasing the hold causes an immediate injection. The signal must remain continuously
(input): active to hold injections. That is, when active, this signal delays an imminent injection
until this line goes to the inactive state. You can use this function with external equipment
to precisely control the timing of the injection valve activation. You can select the active
level (Hi or Lo) of this input in the Input Polarity menu.

2 Installation
Table 1. Input and output pin assignments (Sheet 2 of 2)

Pin # Assignment
Pin 8 Use this pin to signal to other devices that the autosampler is in a READY condition.
A/S READY
(output):
Pins 9 thru 12 Use these user-programmed outputs to trigger column-switching valves or other external
TF1-TF4 hardware. The time functions defined in the currently active file control these outputs (see
(timed outputs): “Timed Events Menu” on page 72).
Recommended Hardwire Connections for a Stand-Alone System

The recommended setup for a stand-alone LC system requires a pump, autosampler, UV/VIS
or fluorescence detector, and an integrator. For best results, connect the following signals:
• Pump Ready
• Inject Hold (detector ready)
• Detector Run/Start
• Integrator Run/Start
To wire the appropriate pin connections, see Table 2. Pin connections for the
SpectraSYSTEM modules are indicated in parentheses.
Table 2. Pin connections for a stand-alone system
Autosampler
Pump Detector Integrator
(pin connection)
Ground (1) Ground (3) Ground (9) (11) Ground (B1)
Pump Stop (3) Pump Stop (5) N/A N/A
(pulsed output)
Pump Ready (5) Pump Ready (1) READY (4) N/A
(input)
Inject Out (6) N/A RUN/START (10) RUN/START "A" (B5)
RUN/START "B" (B14)
Inject hold (7)* Sync (8) N/A N/A
Gradient Start (4) Run Grad (7) N/A N/A
*
Indicates optional connections
Figure 29 illustrates the hardwire connections for the SpectraSYSTEM modules.

2 Installation
Figure 29. Hardwire connections for the SpectraSYSTEM modules

J4
F 1.0 V F /S
C H1
E G round
B 1.0 V F /S
C H2
A G round
TB1 P2 J2
1 P ump R eady
P ump R eady 5 P ump R eady
R eady
4 + +
- -
C H. A C H. B
3 G round
G round
1 G round
G round
9
Run Start Cable
5 P ump S top
P ump S top 3 11 Ground
R un G rad
7 G radient
S tart
4
Integrator
S ync
8 Inject Hold 7
"A" Run Start
Pump 6 Inject Out
R un/S tart
10
"B " Run Start
Autosampler Detector
Communications Menu Parameters

For normal stand-alone operation, you do not need to change any of the values in the
Communications menu. Keep the communications parameters set to the default values (see
Figure 30). The following details for changing the polarity are provided for reference only.
Figure 30. Communications menu with the default values for stand-alone operation

2 Installation
These are the allowable entries and default values for the Communications parameters.
Parameters Allowable entries Default values

Baud Rate 1200, 2400, 4800, or 9600 Bd 9600 Bd
Parity None, Even, or Odd None
Flow Control None or XON/OFF None
Data Bits 8 or 7 8
Stop Bits 1 or 2 1
Echo On or Off On
Y To access the Communications menu
From the OPTIONS menu, select Communications.
Tip If the Communications menu does not appear as one of the OPTIONS menu
choices, return to OPTIONS > Configurations, and verify that Mode is set to Stand
Alone. The Communications field does not appear in the OPTIONS menu if Mode
is set to SpectraNET.
Setting the Polarity of the Autosampler Signals

From the OPTIONS menu you can change the polarity of your autosampler's input and
output signals as required by your other LC system modules. For example, when shipped, the
Autosampler Ready Output is set to send a positive voltage (Hi) when the instrument is ready.
If you change the Autosampler Ready Output Polarity to Lo, the instrument sends a 0-volt
signal (Lo) when it is ready.
The following procedures explain how to change the polarity of the input and output signals.
Y To change the polarity of an input signal
1. From the OPTIONS menu, select Input Polarity.

2. Press the [+] and [–] keys to select either Hi or Lo for the desired input signal shown in
Figure 31.
Figure 31. Input Polarity menu
This menu shows the level for the active state for each input signal.
Tip To determine the current state of a particular signal, return to the main menu,
and select TESTS > Display Input States.

2 Installation
Y To change the polarity of an output signal
From the OPTIONS menu, select Output Polarity. Press the [+] and [–] keys to select
either Hi or Lo for the desired output signal shown in Figure 32.
Figure 32. Output Polarity menu
This menu shows the level for the active state for each output signal.
Tip To determine the current state of a particular signal, return to the main menu,
and select TESTS > Display Output States.
Table 3 and Table 4 show the output signal levels relative to the polarity settings and
instrument status for the autosampler's input and output signals, respectively.
Table 3. Input signal levels
Signal State Polarity
Hi Lo
Pump Ready Ready Hi* Lo
Not Ready Lo Hi
Inj Hold Active Hi Lo*
Inactive Lo Hi
*
Default settings
Table 4. Output signal levels

Signal State Polarity
Hi Lo
Autosampler Ready Ready Hi Lo*
Not Ready Lo Hi
Inject Out Active Hi Lo
Inactive Lo Hi*
Gradient Start Active Hi Lo
Inactive Lo Hi*
Pump Stop Active Hi Lo
Inactive Lo Hi*
*
Default settings

2 Installation
Stand-Alone Communication to Integrators

If you are connecting the SpectraSYSTEM LC to an integrator, two specialized
communication setups are available:
• Through an autosampler-to-integrator cable to ChromJet or DataJet integrators
• Through a binary-coded decimal (BCD) interface to older Thermo Scientific integrators
or to non-Thermo Scientific Integrators
Before using either of these communications setups, you must configure your autosampler as
a stand-alone module.
Y To configure your autosampler as a stand-alone module
1. Turn on your autosampler, wait for the power-up sequence to complete, and then press
the MENU key. Select OPTIONS > Configurations to access the Configurations menu
(see Figure 33).
Figure 33. Configurations menu with the Mode field set to Stand Alone
Sample Syringe 250
Prep Installed No
---------------------------------------------------------
Oven Installed Yes
File Name Protect
1: Off
2: Off
3: Off
4: Off
Mode Standalone
Stand Alone
2. Select the Mode field, and press the [+] and [–] keys to select Stand Alone. Then press
the ENTER key to accept the field value and exit the Configurations menu.
Your autosampler is now configured as a stand-alone LC module.

2 Installation
ChromJet or DataJet Communication

Using an autosampler-to-integrator cable available from Thermo Fisher Scientific, you can set
up your autosampler to send vial information to a Thermo Scientific ChromJet (SP4400) or a
DataJet (SP4600) integrator. For this connection you must have an RJ-45-to-RJ-45 cable and
an integrator adapter (P/N A3981-010).
Y To connect an integrator to the autosampler
1. Turn off your integrator.

2. Insert the RJ-45 connector (telephone connector) into the COMM port (telephone jack)
on the back panel of the autosampler.
3. Connect the adapter to the other end of the cable. It orients in only one direction.
4. Plug the adapter-cable end into your DataJet or ChromJet integrator.
5. Turn on your integrator and type the following:
• BAUD 9600
• POKE#C12D,#FF
6. Hold down the CTRL key and press CALIB.
IMPORTANT You must reenter this sequence after any integrator soft reset. For more
information, refer to the manual supplied with the integrator.
This sequence provides you with the four-line report from your autosampler shown in
Figure 34.
Figure 34. Vial location and injection report
BCD Communication
The BCD communication option provides BCD communication from the SpectraSYSTEM
AS3000 autosampler to older Thermo Scientific and non-Thermo Scientific integrators and
computers. This option provides tray- or vial-location information (or both) to devices
requiring either binary or binary-coded decimal data. If ordered after initial instrument
delivery, the BCD assembly must be installed by a Thermo Fisher Scientific service
representative. Installation instructions are provided in the BCD Option Kit. Contact your
representative for further information.

2 Installation
Ready Participation
Because Enable is the factory setting for all of the selections on the Ready Participation menu,
the Status screen indicates that the autosampler is ready for operation when these conditions
are satisfied:
• The door is closed.
• The column oven is at the set temperature.
• The temperature controller for the tray compartment is at the set temperature.
Customize the settings on the Ready Participation menu to meet your needs.
Y To change the settings on the Ready Participation menu
1. From the main menu, select OPTIONS > Ready Participation.

The Ready Participation menu appears (see Figure 35).
Figure 35. Ready Participation menu
2. To change any of the above requirements, select the appropriate line, and press the
[+] and [–] keys to change ENABLE to DISABLE.

2 Installation
Performance Verification
Hardware Configurations
Your AS3000 autosampler is shipped with a 100 μL sample loop and a 250 μL sample syringe.
You can change the syringe sizes from the Configurations menu (see Figure 36). This menu
also reflects your other installed options (for example, the oven temperature control). If you
want to adjust the rate at which fields cycle through the available choices, you can change the
Key Repeat Rate entry. “Protecting Files” on page 91 discusses the File Protect function also
available from this menu.
Figure 36. Configurations menu
Sample Syringe 250
Prep Installed No
---------------------------------------------------------
Oven Installed Yes
File Name Protect
1: Off
2: Off
3: Off
4: Off
Mode SpectraNet
After you install your SpectraSYSTEM autosampler, run a standard sample, such as a
0.5 percent mixture of toluene in methanol, to verify the instrument's proper operation. In
addition, you can use the following procedures to test your instrument's reproducibility and
sample carryover, and to troubleshoot and maintain the instrument in the future.
Tip Before beginning the performance verification runs, you might want to familiarize
yourself with the autosampler's command center if you are controlling the autosampler in
the Stand Alone mode.
For information on the autosampler’s command center, see Chapter 3, “Keypad

Controls.”

• “Reproducibility” on page 50
• “Sample Carryover” on page 52

2 Installation
Reproducibility
Use this procedure to measure your autosampler's injection reproducibility. In this procedure,
you inject several volumes of a standard sample of 0.5 percent toluene/MeOH, determine the
percent relative standard deviations (%RSD) for the injection volumes, and compare them
with the desired results included in this section. The test takes approximately three hours.
Retain these results for comparison to troubleshoot the injection system, if necessary.
Use the chromatographic conditions listed in Table 5 to test the autosampler’s injection
reproducibility.
Table 5. Injection reproducibility test method
Column: 4.6 × 100 mm Spheri-5 RP18, 5 micron
Flow rate: 1.5 mL/minute
Mobile phase: 100% HPLC-grade methanol
Flush solvent: 100% HPLC-grade methanol
Test sample: 0.5% toluene in methanol (v/v)
Detection: 254 nm
Run time: 3 minutes
Test Setup
Y To set up the test run
1. Fill five vials with the test sample and place them in tray positions A01 through A05.
2. Check for leaks.
3. Initialize your pump.
4. Prepare your detector for a run.
5. If you are not acquiring data through a data system computer, prepare your integrator.
6. Inspect all sample lines for bubbles. (Be sure to check the Teflon line that connects to
port 3 of the injection valve.)
7. Do one of the following:
• If the autosampler is set up as a stand-alone module, go to step 8.
• If the autosampler is controlled from a data system, go to step 9.
8. For stand-alone operation, do the following:
a. Create a file using the Injection menu parameters shown in Figure 37.

2 Installation
Figure 37. Injection menu performance verification parameters
b. Return to the Edit menu.

c. Access the More menu and verify that the Needle Height is set to 2.0. (Do not
change any other parameters in this menu.)
d. Return to the main menu and load your file.
e. Press the SAMPLES key and set up a sample queue that contains five sample sets of
one vial each. For each sample set, enter the following Sample menu values:
Inj/Sample 10
Cycle Time 1.5
No. Vials 1
Vary the injection volume (Inj Vol) for each set using the values listed in Table 6.
Table 6. Reproducibility test sample queue parameters
Sample set Inj Vol. (μL) Sample vial
1 10 A01
2 1 A02
3 3 A03
4 7 A04
5 10 A05
f. Return to the main menu.

g. Flush the syringe with 500 μL of flush solvent. From the main menu, select
COMMANDS > Flush Sample Syringe.
h. Press the RUN key.
9. For SpectraNet control, do the following:
a. Use the partial loop injection method for the autosampler and the method
parameters listed in Table 5.
b. Set up a sequence that makes 10 injection per sample using the injection volumes and
sample vial locations listed in Table 6.
c. Start your sequence run.
The autosampler makes 50 injections. The first group of ten injections is used to equilibrate
the system, so do not use the data from these injections.

2 Installation
Test Results—%RSDs
Determine the percentage of relative standard deviations (%RSD) for the injection volumes
and compare them with the desired results in Table 7.
Table 7. %RSD results for the reproducibility test
Volume (in μL) %RSD
1 <1*
3 <0.7*
7 <0.5*
10 <0.5**
* Typical value
** Instrument
specification
If your results are other than expected, see Chapter 7, “Troubleshooting.”
Sample Carryover
Use this procedure to verify that the sample carryover is below the 0.01 percent specification
for your autosampler. It requires the use of silicon septa, the appropriate volume of the
required flush solvent, and clean (not previously used) blanks. The procedure minimizes the
effects of sample concentration or chemistry, chromatographic conditions, detector linearity,
or other hardware characteristics that might affect sample carryover.
This procedure is independent of sample- and system-specific characteristics. It reduces

sample effects including extinction coefficients, chemical interaction with other sample or
system components (the column), and sample degradation. It also minimizes system effects
including detector linearity, pump and mixing anomalies, and column and guard-column
contamination.
In this procedure you inject your sample using the push loop injection type, a subsequent
blank (BLANK1), additional blanks to return the system to baseline, and then a standard
(STANDARD) that is 0.01 percent of your sample. You determine the carryover percentage
by multiplying the ratio of the carryover by the 0.01 percent specification:
Carryover = [Peak AreaBLANK1/Peak AreaSTANDARD] × 0.01%
If desired, run this procedure three times to replicate the results.

2 Installation
Carryover Test Materials

Performing this procedure requires the following:
• Your sample
• 21 vials, septa, and caps
• Autosampler
• Any HPLC pump, detector, and data system
Carryover Test Sample Preparation
Y To prepare your sample and standard
1. Place appropriate volumes of sample and starting mobile phase into a vial labeled
SAMPLE.
2. Dilute your sample 10000-fold in starting mobile phase and pipette into a vial labeled
STANDARD.
Example:
1. The sample is 100 mg protein in 1 mL phosphate buffer (SAMPLE).
2. Transfer 1 μL of SAMPLE into a 10 mL volumetric flask and dilute to volume with
phosphate buffer (STANDARD).
Carryover Test Blank Preparation
Y To prepare your blanks
1. Pipette fresh starting mobile phase into three sets of five vials.
2. Label vials as BLANK, BLANK1, BLANK2, BLANK3, and BLANK4 for each test set.
Carryover Test Procedure
Y To set up your system
1. Prepare the appropriate mobile phase or phases.

2. Set up the appropriate chromatographic conditions for your sample.
3. Set up your integrator/data system so that it displays retention times and peak area
information.

2 Installation
Y To set up the autosampler injection parameters
1. Set the flush volume to 2000 μL and the injection type to PushLoop.
Tip To set the flush volume and the injection type from the keypad controls, press the
MENU key, and then select Files > Edit > More. Scroll down and select Flush
Volume. Press the [+] or [–] keys to select 2000 μL. Scroll and select Injection Type,
and then select Push Lo.
2. Enter an appropriate injection volume.

Enter an injection volume no greater than 40 percent of the nominal sample loop size.
For example, for a 100 μL sample loop, do not enter an injection volume greater than
40 μL.
Tip To enter the injection volume from the keypad controls, press the MENU key,
and then select Files > Edit > Injection. In the Injection Volume field, use the [+] and
[–] keys to enter the injection volume.
3. Set the number of injections to 1.
Tip To enter the number of injections from the keypad controls, press the MENU
key, and then select Files > Edit > Injection. In the Injections/Sample field, use the
[+] and [–] keys to enter 1.
IMPORTANT Make sure that the sample is soluble in the flush solvent. For best
results, use the same solvent composition for the flush solvent and the mobile phase.
Y To inject the sample set
1. Place the vials in the tray as follows:

A01: BLANK
A02: SAMPLE
A03: BLANK1
A04: BLANK2
A05: BLANK3
A06: STANDARD
A07: BLANK4
(Add additional Blanks as necessary to return the detector signal to baseline before
replicating the test.)
2. Set up a sequence or an autosampler file to make one injection per vial.
3. (Optional but recommended) Set up two additional groups of seven vials to run the
carryover test in triplicate.
4. Run your HPLC system using the appropriate chromatographic conditions for your
sample.

2 Installation
Carryover Calculation
Y To calculate the percentage of sample carryover
1. Divide the peak area of BLANK1 by the peak area of the STANDARD. This gives you
the ratio of the carryover to the 0.01% specification.
2. Multiply this value by 0.01% to obtain the carryover percentage.
Example:
If the peak area for BLANK1 is 110958 counts,
and the Peak area for the STANDARD is 656283 counts,
the ratio of the carryover to the specification is 110958/656283 or 0.1691.
% carryover = 0.1691 × 0.01%
% carryover = 0.001691

3
Keypad Controls
This chapter introduces you to the autosampler's command center, provides you with three
basic rules for using the keypad controls to navigate through the menu screens, and shows you
how to make an injection using the keypad controls.
For more information on using the keypad controls, see Chapter 4, “Standalone Operation
from the Command Center.” If you are controlling the autosampler from a data system
computer, refer to the Help provided with the data system for information on operating the
autosampler.
Before you start this chapter, be sure that you read the Safety Information section and install
your autosampler as described in Chapter 2, “Installation.”
Contents
• Command Center
• Keypad Functions
• Menus and Screens
• Messages
Note As you proceed through this chapter, you can explore the general architecture of
your autosampler’s menus and screens. You can also use this topic “SpectraSYSTEM
AS3000 Menus” on page 151 as a guide.
To make your first injection, follow the procedures in “Standalone Operation from the
Command Center” on page 63 or this two-page guide “Quick Start: Starting Runs from
the Command Center” on page 155.
Command Center
The SpectraSYSTEM autosampler has a keypad and two-line display on the front panel
(see Figure 38). This is the command center where you access menus and control the
instrument's operations.

3 Keypad Controls
Command Center
Figure 38. Command center for the SpectraSYSTEM autosampler
FILES QUEUE TESTS

COMMANDS OPTIONS
RUN STATUS MENU
STOP
ENTER
Samples SpectraSYSTEM AS3000
Navigating the autosampler menus assumes these three rules:

1. The arrow keys , , , move the cursor in the direction printed on the key.
Tip Press the MENU key to jump quickly to the top of the menu structure.
2. The shape of the cursor determines how you make a selection:

• If a triangular cursor appears, press the ENTER key.
• If a blinking square cursor appears, press the [+] or [–] keys to scroll up or down
through preset choices, or to increase or decrease alphanumeric entries.
3. There are four ways to accept (and automatically save) an entry. Move the cursor out of
the field by any of the following methods:
• Pressing the ENTER key
• Using the arrow keys
• Pressing the MENU key
• Pressing the STATUS key
Note You cannot leave a menu if errors are present or if you have not completed all
the necessary entries.

3 Keypad Controls
Keypad Functions
The autosampler display follows these conventions:

• Top-level menu choices appear in all-capital letters, except for Samples.
• A field's square cursor changes to an underscore cursor when you scroll through preset
choices or enter numerical values and characters.
• A solid arrow, , on the right side of some displays indicates that the current menu
continues on additional screens. To access additional menu lines, press the
DOWN ARROW key ( ) on the keypad.
• The last line of a longer menu is frequently a blank display line (without a solid
arrow, ).
Keypad Functions
The keypad of each SpectraSYSTEM instrument consists of twelve keys. Four keys directly
control the instrument's operation: RUN, STOP, STATUS, and, on the autosampler, a blank
key called Samples. The remaining keys either access commands (MENU and ENTER), or
are used to set parameters and move around the display keys ( , , , , [+], [–]).
Table 8 describes each key’s function.

Table 8. SpectraSYSTEM keypad functions (Sheet 1 of 2)
Keys Functions
RUN Starts the run. The specific RUN operation depends on the contents
of the sample queue:
• If there are sample sets (groups of sample and associated
calibration vials) in the sample queue, pressing the RUN key
begins processing the first vial in the sample set.
• If the sample queue is empty, pressing the RUN key prompts you
to press the Samples key to display the Samples menu so that you
can add sample sets to the sample queue.
STOP Pauses the sample set currently running, cancels subsequent sample
sets, and returns the autosampler to the initial run conditions. For
more information on the STOP key's function, see Chapter 4,
“Standalone Operation from the Command Center.”
STATUS Displays the Status screen. From the Status screen you can monitor the
run in progress.
Note Unlike the other SpectraSYSTEM instruments, on the
autosamplers you can make changes to the run in progress from the
Samples key rather than from the STATUS key (see below).

3 Keypad Controls
Keypad Functions
Table 8. SpectraSYSTEM keypad functions (Sheet 2 of 2)

Keys Functions
Samples The only variable key (unlabeled) in the whole SpectraSYSTEM
family. (It has a different function on each of the SpectraSYSTEM
modules.) On the autosampler, the blank key is the Samples key whose
name appears on the nameplate below it.
The Samples key displays the Samples menu, which you use to define
the resources (samples, reagents, and standards) and assign a file to
each sample set. From the Samples menu you also add sample sets to
the sample queue.
Because you manage resources and files from the Samples menu, the
Samples key gives you the real-time editing capability provided by the
STATUS key on the other SpectraSYSTEM instruments. That is, from
the Samples menu you can make changes to the file that is currently
running. By pressing the Samples key during a run, you can obtain
information about, or edit the locations and injection volumes of, the
sample and calibration vials. Chapter 4, “Standalone Operation from
the Command Center,” contains more information on the Samples
key.
MENU Displays the main menu (see Figure 39). For more information, see
“Main Menu” on page 61.
ENTER Accepts a selection or menu entry. The ENTER key also advances the
cursor to a new field, either in the same line of the display or in the
line below.
, , , The arrow keys (UP, DOWN, LEFT, or RIGHT) move the cursor in
the direction indicated on the key. The UP and DOWN ARROW
keys also move the cursor between menus and displays.
[+] and [–] Scroll through a field's available choices, or changes the value of
alphanumeric entries. Holding down either key continuously scrolls
the list of choices forward or backward until you release the key.
In fields that require alphabetical or numerical entries, the value of

each digit is increased or decreased by one unit each time you press the
[+] or [–] key. In fields that accept either numeric or character entries,
such as the File Name field, the [+] and [–] keys scroll through the
alphabet from A to Z; then through the numbers 0 to 9; and finally to
a slash, hyphen, and blank space.
In other fields, the [+] key advances you through a preset list of choices
while the [–] key takes you back through the list.

3 Keypad Controls
Menus and Screens
Menus and Screens

Your autosampler has two kinds of displays: menus and screens. Menus require you to make
selections or enter specific values. Screens display read-only information. The menu tree at the
back of your manual (see “SpectraSYSTEM AS3000 Menus” on page 151) illustrates the
structure and content of the autosampler's menus and screens.
Main Menu
The main menu (see Figure 39) is the top level of the menu structure. It gives you access to
five other menus: FILES, COMMANDS, QUEUE, OPTIONS, and TESTS. To see the
main menu, press the MENU key at any time.
Figure 39. Main menu accessed with the Menu key
The tasks associated with each menu follow:

Files menu Edit, load, or delete files.
Queue menu Edit or change the order of sample sets in the sample queue.
Tests menu Run built-in instrument diagnostics.
Commands menu Run built-in instrument routines.
Options menu Set up or change the autosampler’s configuration.
For more information on any of the autosampler’s menus, see Chapter 4, “Standalone
Operation from the Command Center,” and Chapter 5, “Diagnostic Procedures.”
Status Screen
The Status screen automatically appears whenever you turn on the instrument or press the
STATUS key. The Status screen (see Figure 40) displays the status of the sample queue, the
current sample set, the current sample vial, and the total number of samples in the set.
Figure 40. Queue Status screen
Pressing the DOWN ARROW key ( ) displays the Injector Status screen (see Figure 41).
Figure 41. Injector Status screen

3 Keypad Controls
Messages
Pressing the DOWN ARROW key ( ) a second time displays the Oven Temperature Status
screen (see Figure 42).
Figure 42. Oven Temperature Status screen
Chapter 4, “Standalone Operation from the Command Center,” contains more information
on the Status screen.
Messages
Three different kinds of messages can appear on your autosampler's display: user messages,
confirmation messages, and error messages.
User Messages
User messages tell you about an existing instrument condition or ask for further actions. Some
of these messages only appear on the display for three seconds. All user messages have a single
asterisk before and after them. Figure 43 shows an example of a user message requiring further
action.
Figure 43. User message example
Confirmation Messages
A confirmation message appears for one second after the successful completion of an
operation. All confirmation messages have a pair of asterisks before and after them.
Figure 44 shows an example of a confirmation message.
Figure 44. Confirmation message example
Error Messages
An error message appears when the autosampler encounters an undesirable condition that
prevents it from carrying out an operation. All error messages have a pair of exclamation
points before and after them. An error message remains on the screen until you press a key.
Figure 45 shows an example of an error message.
Figure 45. Error message example

4
Standalone Operation from the Command Center

This chapter describes how to use the autosampler’s front panel controls to specify the
injection parameters for your chromatographic methods and the vial locations for your
injection sequences. Use these controls if you are not controlling the autosampler from a
chromatography data system.
If you are controlling the autosampler from a chromatography data system, use the data
system to create methods with the appropriate injection parameters and to create injection
sequences with the appropriate vial locations. For information on controlling the
SpectraSYSTEM autosampler from the data system, refer to the Help provided by the data
system.
Before beginning this chapter, be sure that you have completed the Startup Checklist found in
the beginning of this manual, installed your instrument according to the procedures described
in Chapter 2, “Installation,” and understand the keypad controls as described in Chapter 3,
“Keypad Controls.”
Contents
• Run Preparation
• Starting a Run by Pressing the Run Key
• Monitoring the Run Status
• Changing the Run in Progress
• File Management
• Needle Height
• Optimization
• Special Commands in the Commands Menu

4 Standalone Operation from the Command Center
Run Preparation
Run Preparation
Using the front panel controls for the SpectraSYSTEM autosampler, you can process up to
39 non-priority sample sets (groups of sample vials and associated calibration vials) within a
given run.
This section covers the following procedures, along with the instrument's file-management
features.
• “Creating a File” on this page
• “Saving a File” on page 77
• “Loading a File” on page 77
• “Building a Sample Queue” on page 78
• “Entering Your Other LC Parameters” on page 81
IMPORTANT Be sure that your sample or samples are completely soluble in the mobile
phase and that you have filtered your samples and solvents through a 0.45-micron filter.
These techniques minimize sample precipitation in the lines and remove any particulate
matter that could obstruct the flow through the autosampler's injection valve or the LC
column. Fill the solvent reservoir with flush solvent.
Creating a File
A file contains the autosampler parameters applied to a specific sample set.
You can create up to four unique files numbered 1 through 4. From the Edit menu, you can
name your file and access additional menus to enter injection, calibration, timed events, and
other run parameters.
Tip The following procedure describes how to create an edit file. For information on
starting a run, see “Loading a File” on page 77.
Figure 46 shows the Edit menu. Selecting the Injection, Calibration, Timed Events, or More
item opens an additional menu.
Figure 46. Edit menu
Edit File 1
File Name
---------------------------------------------------------
Injection
Calibration
Timed Events
More

Run Preparation
Y To create a file
1. Specify a number and a name for the file.

a. Press the MENU key.
b. Select FILES > Edit.
The Edit menu appears (see Figure 46 on page 64).
c. In the Edit File field, select 1, 2, 3, or 4.
The file number identifies the file.
The Edit File field indicates the number of the selected file. File 1 automatically appears
in this field when the Edit menu is first displayed. If you want to edit a different file, press
the [+] and [–] keys to select a different file number.
2. (Optional) In the File Name field, enter a name for this file.
When you first display the Edit menu, the File Name field contains eight blank
characters. Press the [+], [–], UP ARROW , and DOWN ARROW keys to create
a file name using the following characters: A to Z, 0 to 9, \, blank, dash, or hyphen.
3. Select the injection type as follows:
a. Press the DOWN ARROW key ( ) until the cursor reaches the More menu item,
and then press ENTER.
b. Press the DOWN ARROW key ( ) until the cursor reaches the Injection Type
menu item, and then press ENTER.
c. Select the injection type.
4. Make the appropriate entries in these menus:
• “Injection Menu” on page 66
• “Calibration Menu” on page 69
• “Timed Events Menu” on page 72
• “More Menu” on page 74
When you exit the file, the autosampler automatically saves the file.

Run Preparation
Injection Menu
Use the Injection menu to specify the injection volume, the number of injections per sample,
the time between injections, and the temperature of the autosampler’s controlled temperature
zones.
Figure 47 shows the Injection menu and Table 9 describes the parameters in the Injection
menu.
Figure 47. Injection menu (AS3000 autosampler)
Injection Volume 10.0
Injections/Sample 1
---------------------------------------------------------
Cycle Time 10.0
Oven: OFF_ Temp 18
Tray Temp: OFF_ Temp 18
Y To specify the injection parameters
1. From the main menu, choose File > Edit > More.
2. Select the appropriate injection type (see “More Menu” on page 74).
3. Choose File > Edit > Injection.
4. In the Injection Volume field, do one of the following:
• For the full-loop injection type, select the appropriate loop size.
The selections depend on the syringe size (see “Injection Volume or Loop Size” on
page 67).
• For the pull-loop injection type, enter an injection volume from 0.1 to 212 μL for
the 250 μL syringe.
• For the Push Lo injection type, enter an injection volume from 0.1 to 10 μL.
• For the Push Hi injection type, enter an injection volume from 0.1 to 200 μL.
5. In the Injections/Sample field, enter the number of injections that you want the
autosampler to make per sample vial.
6. In the Cycle Time field, enter the initial time between injections.
7. In the Oven field, select On to activate temperature control, and then enter the
appropriate column oven temperature from 15 to 80 °C, in one-degree increments.
8. In the Tray Temp field, select On to activate temperature control, and then enter the
appropriate tray compartment temperature from 0 to 60 °C, in one-degree increments.
After you complete the injection parameters, the cursor moves to the Calibration menu
item.

Run Preparation
Table 9. Injection menu parameters (Sheet 1 of 2)

Parameter Description
Injection Volume or Specifies the injection volume or the loop size.
Loop Size
The selections or range depends on the injection type and the syringe size.
Injection Type Selection or range
Loop Size The selections depend on the syringe size.
(Full-loop injection) Syringe size Selections
250 μL 5, 10, 20, 50, and 100 μL
500 μL 5, 10, 20, 50, 100, and 200 μL
1000 μL 5, 10, 20, 50, 100, 200, and 500 μL
2500 μL 5, 10, 20, 50, 100, 200, 500, and 1000 μL
5000 μL 5, 10, 20, 50, 100, 200, 500, and 1000 μL
IMPORTANT Be sure that the Loop Size field value reflects the
size of the sample loop.
Pull The maximum injection volume depends on the syringe size.
Syringe size Maximum injection volume
250 μL 212 μL
500 μL 461 μL
1000 μL 956 μL
2500 μL 1500 μL
5000 μL 1500 μL
Push Hi Range: 0.1 to 10.0 μL
Push Lo Range: 1 to 200 μL
IMPORTANT For a variable-loop injection, limit the injection
volume to approximately one-half the sample loop size.
Injections/Sample Specifies the number of injections to be made from each vial (1 to 99).

Run Preparation
Table 9. Injection menu parameters (Sheet 2 of 2)

Cycle Time Specifies the time (0 to 655.3 minutes) between injections (from the injection to the end of
the run). In calculating this value, be sure to allow enough time for the column to
equilibrate (if you are running a gradient), for all peaks to elute from the column, and for
the integrator to print any post-run reports and perform any post-run calculations.
The autosampler is capable of making an injection approximately every 90 seconds,

depending on the injection and flush volumes selected. If a Pump Ready contact closure
controls your cycle time, you may set the Cycle Time to 0.0.
Tip The default flush volume is 400 μL so that the total injection cycle time (including
the flush cycle) is approximately two minutes.
Column Oven Appears only if the Column Oven is set to ON in the Configurations menu.
Selections: On or Off
Temperature range: 15 to 80 °C, in one-degree increments
Tip
• You can specify temperatures starting at 5 °C above ambient.
• When you set the oven's state to On, the oven does not activate (turn on) until you
load your file.
• The autosampler automatically delays the start of the run until the oven reaches the
set temperature. Once activated, the oven requires about 15 minutes to reach a
temperature of 70 °C. To save time, you might want to load your file so that the oven
can be warming up while you are completing your run preparation and entering the
file parameters for your run. For more information on loading your file, see “Loading
a File” on page 77.
Tray Temperature Appears if the Tray Temperature is set to ON in the Configurations menu.
Control
Selections: On or Off
Temperature range: 0 to 60 °C, in one-degree increments
For more information, see “Autosampler Components” on page 2.

Tip
• When you set the tray temp state to On, the tray temperature controller does not
activate (turn on) until you load your file.
• Once activated, if empty, the tray compartment requires about 30 minutes to reach a
temperature of 0 °C and about 10 minutes to reach a temperature of 60 °C. To save
time, you might want to load your file so that the tray compartment can be warming
up while you are completing your run preparation and entering the file parameters for
your run. For information on loading your file, see “Loading a File” on page 77.

Run Preparation
Calibration Menu
Use the Calibration menu to set up the calibration parameters, such as the number of
calibration levels and the number of sample injections between calibration sets, for your
sample set.
Note You specify the numbers of samples per sample set and the vial locations for samples
and calibration standards in the Samples menu.
Figure 48 shows the Calibration menu and Table 10 describes the parameters in the
Calibration menu.
Note The data system that you use to acquire and process your data files does not
recognize the information that you enter in the Calibration menu. To process your data
files, you must create an appropriate processing sequence from your data system that
contains the appropriate sample and calibration information.
Figure 48. Calibration menu
Y To specify the injection settings for the calibration vials
1. From the main menu, choose File > Edit > Calibration.
2. In the Number of Levels field, select the number of calibration levels for your application.
3. In the Samples/Calibration field, select the number of sample vials between calibration
vials.
4. In the Injections/Level field, select the number of injections that you want the
autosampler to make from each calibration vial.
5. In the Injection Volume or Loop Size field, select the injection volume for the calibration
vials or the loop size (full-loop injection type).
For information on the injection volume range or loop size selections, see “Injection
Volume or Loop Size” on page 67.

Run Preparation
6. In the Type field, specify whether you want the autosampler to reuse one set of vials for
the calibration standards or a new set of calibration vials for each calibration set:
• To specify a single location for the calibration vials, select Reuse Same Vials.
If you select Reuse Same Vials, load only one set of calibration vials in the sample
trays. Specify the location of the first calibration vial in the Samples menu. The
autosampler determines the number of calibration vials based on your entry in the
Number of Levels field (see Table 10).
• To specify a new set of calibration vials for each calibration set, select Intersperse
Vials.
If you select Intersperse Vials, load the trays with a set of calibration vials for each
calibration set as specified in the Samples/Calibration entry. Specify the location of
the first calibration vial in the Samples menu. The autosampler determines the total
number of calibration vials based on your entries in the Number of Levels,
Samples/Calibration, and Bracket Samples fields (see Table 10).
7. In the Bracket Samples field, select Yes or No.
After you complete the injection parameters, the cursor moves to the Timed Events menu
item.
Table 10. Calibration menu parameters (Sheet 1 of 2)
Number of Levels Specifies the number of calibration levels (0 to 9).
The autosampler automatically copies this value to the Calib 1Vial 1 (of X) field, in the
Samples menu, where X equals the number of levels. (For more information, see Calib Vial
1 (of X) on page 79.) A value of zero in the Number of Levels field indicates that there are
no calibration injections for the specified sample set.
Samples/Calibration Specifies the calibration interval (the number of sample vials to be injected between each
recalibration).
Injections/Level Specifies the number of injections (1 to 99) from each calibration level (0 to 9).
Injection Volume or See the information on the Injection Volume or Loop Size parameter in the Injection menu
Loop Size (Table 9 on page 67).

Run Preparation
Table 10. Calibration menu parameters (Sheet 2 of 2)

Type Specifies one of two types of patterns for determining the location of the calibration vials:
Pattern Use
Reuse Same Vials Programs the autosampler to use the same calibration vials each time a
recalibration is made. When a calibration is required, the autosampler
goes to the first calibration-vial position specified in the Sample menu
and injects all the calibration vials. It then injects the number of
samples indicated in the Calibration menu for Samples/Calibration.
Intersperse Vials Programs the autosampler to use each calibration vial only once. You
must manually intersperse your calibration vials between your sample
vials within the sample set. The autosampler makes injections in
tray-placement order.
You specify the location of the first calibration vial in the Samples
menu. The autosampler uses the value that you enter in the
Samples/Calibration field to determine the location of subsequent
calibration vials.
Bracket Samples Specifies whether or not you want to automatically end the sample set with a recalibration.
If you select Yes, the autosampler processes the last sample and then repeats the calibration
series specified for the sample set. If you select No, the autosampler stops and returns home
after it injects the last sample.
Table 11 shows the injection sequence when you select either the Reuse Same Vials or the
Intersperse Vials calibration routines, as well as the injection sequence when you select
Bracket, for the following sample set:
• Number of samples: 4
• Calibration levels: 2
• Number of samples between each calibration set: 2
• First calibration location: A01
• First sample location: A03
Use the Calibration menu to specify the number of calibration levels per calibration set and
the number of samples between calibration sets. Use the Samples menu to specify the number
of samples and the vial locations for samples and calibration standards.
Note The autosampler does not send the calibration and sample information to your
integrator or data system. To analyze the results of the injection set, you must reenter the
calibration and sample sequence into your data processing system.

Run Preparation
Table 11. Comparison of the total number of vials used for the calibration routine selections
Injection Reuse vials Reuse vials and Intersperse vials Intersperse vials
bracket and bracket
C A01 A01 A01 A01
C A02 A02 A02 A02
S A03 A03 A03 A03
S A04 A04 A04 A04
C A01 A01 A05 A05
C A02 A02 A06 A06
S A05 A05 A07 A07
S A06 A06 A08 A08
C N/A A01 N/A A09
C N/A A02 N/A A10
Total # of vials 6 6 8 10
Timed Events Menu

Use the Timed Events menu to create a time program to turn on/off external devices (such as
column-switching valves and fraction collectors) at preset times during your run. For timed
events, the autosampler uses pins 9 to 12 from its 12-pin terminal. For information on
connecting external devices to your autosampler, see “Stand Alone Mode” on page 39.
Figure 49 shows the autosampler’s Timed Events menu.

Figure 49. Timed Events menu
The Timed Events menu holds a maximum of nine lines, each of which sets Hi or Lo for one
or more timed event outputs at the times specified. When the TF terminal is set to Hi, it
presents a +5 V signal.
Figure 50 shows a timed events program that does the following:

• At 0.5 minutes, turns on the TF2 terminal.
• At 1.00 minutes, turns off the TF2 terminal and turns on the TF3 terminal.
• At 2.00 minutes, turns on the TF2 terminal and turns off the TF3 terminal.

Run Preparation
Figure 50. The timed events program described above

d
Note The Run-time clock stops and resets at the completion of the Cycle Time. Time
lines longer than the Cycle Time value are never activated.
Y To add a line to the end of the timed events program
1. Press the DOWN ARROW key ( ) to move the cursor to the blank line after the last
displayed line.
2. Press the [+] key to copy the last existing line with a new time incremented by one
minute.
3. Use the arrow keys and the [+] and [–] keys to change the time and set the time functions'
states (Hi/Lo).
Y To delete a line from the timed events program
1. Move the cursor to the Time field in the line to be deleted.

2. Hold down the [–] key until the value is zero (0.00).
3. Press the [–] key once to erase the line.
If you are deleting a line from the middle of a timed events program, the blank line remains
until you move the cursor to another line.
Note If you delete both of the visible lines on the display, both lines disappear, but the
cursor remains. Press the UP and DOWN ARROW keys ( or ) to move to the
remaining lines in the program.
Y To insert a line between two existing lines in the timed events program
1. Move the cursor to the blank line at the end of the program.
2. Enter a time that falls between two existing times.
3. Move the cursor off the new line. The autosampler automatically inserts the new line.
4. Move the cursor to the newly inserted line or lines and set the Timed Events Outputs'
states as desired.

Run Preparation
More Menu
Use the More menu (Figure 51) to enter the remainder of your run parameters.
Figure 51. More menu
Equilibration Time 0.0
Gradient Delay 0.00
---------------------------------------------------------
Viscosity Normal
Flush Volume 400
Injection Type Push
Injection Range .1-10.0
Needle Height 2.0
Table 12 describes the More menu parameters.

Table 12. More menu parameters (Sheet 1 of 3)
Equilibration Time Specifies the length of time (in minutes) required for the column or LC system to
equilibrate. The equilibration time allows time for the column to equilibrate prior to the
first injection of a new sample set. It is only in effect before the first injection. The default
value of 0.0 is a good starting value for many applications.
Gradient Delay Specifies the amount of time required to allow the mobile phase to travel from the pump's
proportioning valve to the column. Use this field only if you are running a gradient. To
determine the gradient delay value, you must calculate the pre-column volume, which is
best done during installation. To calculate your pre-column volume and gradient
delay value, see “Gradient Delay” on page 99.
Viscosity Specifies the sample viscosity (Normal, Medium or Viscous). The viscosity setting affects
the sample syringe draw-rate. A higher viscosity setting automatically decreases the syringe
draw-rate.
Tip Use the Normal setting for running most reversed-phase applications.
Flush Volume Specifies the flush volume.
Range: 200 to 5000 μL

Default: 400 μL

Run Preparation

Injection Type For a description of each injection type and the excess sample volume required for injection,
see “Injection Types” on page 4.
The optimum injection type depends on the amount of sample you have and the degree of
precision desired.
Choose from four different injection types:

Full-loop Full- or fixed-loop injection is useful when you want maximum precision
and have unlimited sample.
The actual injection volume depends on the loop size.

Note If you select full-loop injection, the Injection Volume field in the
Injection menu changes to Loop Size and the Injection Volume field in the
Calibration menu does not appear.
Pull-loop Pull-loop injection (traditional variable-volume injection) is useful when
sample conservation is important and when large injection volumes
(> 100 μL) are required.
Tip Use a sample loop that is at least twice the size of the largest injection
volume. For example, use a 200 μL sample loop or larger to inject
100 μL.
PushLoop PushLoop injection (variable-volume method) gives the precision of
(Push Hi) fixed-loop injection with limited amounts of sample.
PushLoop Use the PushLoop (Push Lo) method for smaller injection volumes
(Push Lo) (< 10 μL).

Run Preparation

Injection Range The Injection Range field displays the injection volume range, depending on the Injection
Type that you select.
Injection type Range
Full-loop Displays the range: 5 to 1000.
During a full-loop injection, the autosampler overfills the sample loop.

The actual injection volume equals the physical size of the sample loop,
which is ± 20 percent of the loop’s nominal size.
Tip When you select the Full Loop injection type, the Edit > Injection > Injection
Volume field changes to Loop Size. The Loop Size selections depends on the configured
syringe size.
Pull-loop Displays the range: 1 to 1500 μL.
Specify the injection volume in the Injection Volume field of the Injection
menu.
PushLoop Displays the range: 0.1 to 10.0 μL.
(Push Lo)
Specify the injection volume in the Injection Volume field of the Injection
menu.
PushLoop Displays the range: 1 to 200 μL.
(Push Hi)
Tip For the variable-volume injection types, specify the injection volume in the Injection
Volume field of the Injection menu.
Needle Height Controls the distance between the needle tip and the bottom of the vial.
Range: 0.0 to 20.0 mm

Default: 2.0 mm

Run Preparation
Saving a File
The autosampler automatically saves your file. Once you have filled in all of the Edit menu
parameters, you have finished creating your edit file. Exiting the Edit menu automatically
saves your file but does not load it. For more about file management, see “File Management”
on page 90.
Note Pressing the RUN key after creating your file does not start your run. You must first
add it to the sample queue. For more information, see “Building a Sample Queue” on
page 78.
Loading a File
Use the Load function when you want to run a single sample set manually, for example, to
turn on your oven or tray heater/cooler.
Y To load an Edit file
1. From the main menu, select FILES > Load.

The Load menu appears.
Figure 52. Load File field

• To load the last file you edited, press the [+] and [–] keys to select its file number and
press the ENTER key.
–or–
• To load a different file, select the correct file number and then press the ENTER key.
The **File Loaded** message appears. Once a file is loaded, it becomes your run file.
You use the Load function to run a single sample set; however, if you want to run a group of
sample sets, press the RUN key from the sample queue. Once you press RUN, the
autosampler automatically loads each file into the queue before running it. You do not need to
manually load each file. For more information on running your samples from the sample
queue, see “Building a Sample Queue” on page 78

Run Preparation
Building a Sample Queue

The sample queue is the list of sample sets and associated files to be run. Building your sample
queue requires adding each item to the queue from the Samples menu and then arranging
those items in the desired run order from the Queue menu. If you run a group of files from
the sample queue, the SpectraSYSTEM application automatically loads each file before it is
run.
To build a sample queue, follow these procedures:

• “Adding Items to the Sample Queue” on this page
• “Changing the Order of Sets in the Queue” on page 80
• “Deleting Sets from the Queue” on page 80
• “Managing a Priority Set in the Queue” on page 81
Adding Items to the Sample Queue
Y To add an item to the sample queue
1. Press the Samples key to access the Samples menu.

2. Enter each of the values shown in the Samples menu (see Figure 53) and described in
Table 13.
Tip Since the method downloads most of the values automatically, the only values
that require editing are those in the File Number and Vial Location fields.
Figure 53. Samples menu

File Number field
Vial Location
fields

Run Preparation
Table 13. Samples menu parameters

Sample Set Specifies the sample set you want to add to the queue. You can add
the sample set only once to the sample queue. You can load a
maximum of 39 sets into the sample queue, plus one priority set.
File Specifies the file number to be applied to the specified sample set.
The file parameters determine the sequence of Sample Set
prompts.
Range: 1 to 4
Injection Volume, These values are copied from the Injection menu of the associated
Injections/Sample, file.
and Cycle Time
Calib Vial 1 (of X) This value is copied from the Calibration menu of the associated
file.
Specifies the location of the first vial in the calibration series.

X is an indicator of the number of calibration levels specified in
the file.
Range: A01 to C35

Tip The vial position automatically wraps.
First Sample Vial Specifies the location of the first sample vial.
Range: A01 to C35

Number of Specifies the number of sample vials in the sample set.
Samples
Range: 1 to 105
Add to Queue Selecting Yes and pressing the ENTER key adds the selected
sample set to the queue. You can add each set only once to the
sample queue.
Selecting No returns you to the Status menu.
3. After filling in the Samples menu for the first sample set, press the Samples key again.
This returns you to the top of the menu where you can add the next sample set.
Figure 54 shows a Queue menu with three sample sets.

Run Preparation
Figure 54. Queue menu with no priority-vial sample sets in the queue
Changing the Order of Sets in the Queue
Y To change the order of the items in the queue
1. Move the cursor to the line where you want to change the order.
2. Increment or decrement the set to the new Order value.
For example, to run sample set 5 before sample set 3, move the cursor to the order
column of the sample-set 5 line, and decrement the Order value to 1 (see Figure 55).
Figure 55. Queue with three sequential sets
Changing the run order of set 5 from third to first
The lines rearrange themselves after you exit the field (see Figure 56).
Figure 56. Queue with reordered sets
Tip You can only change Order 1 if the sample set is not active—that is, when you press
the STATUS key, the QStatus column reads IDLE.
Deleting Sets from the Queue
Y To delete an item from the sample queue
1. Move the cursor to the line containing the item you want to delete.
2. Decrement the Order number to 0 and then blank.
Moving the cursor to another line deletes the blank line from the display.

Starting a Run by Pressing the Run Key
Managing a Priority Set in the Queue

A priority set is inserted into the active set and its samples run before other samples in the
active set. It must be assigned to the active file. It appears in the Queue menu with a P in the
Set field (see Figure 57). You cannot assign or change its priority status from the Queue menu.
A priority set is automatically deleted from the queue upon completion of the active set or
when the queue (QStatus) returns to its IDLE state (if you press the STOP key). For more
information on running priority vials, see “Priority Sample Sets” on page 87.
Figure 57. A sample queue that contains a priority set
Entering Your Other LC Parameters

Prepare your other LC modules for a run and enter the run parameters for your pump,
detector, and data-output device (recorder, integrator, or data system). Before you start your
run, complete these tasks:
• Initialize your pump and degas your solvents as required for your application.
• Be sure your detector is stabilized. Do not start your analysis until you achieve a stable
baseline.
• Set up your data-output device.
For more information on connecting your autosampler to other LC modules, see Chapter 2,
“Installation.”
Starting a Run by Pressing the Run Key

Once you have created and loaded your file, added your sample set or sets to the sample
queue, and installed your sample trays, you are ready to start your run.
Y To start a run
1. Load your sample and calibration vials into the trays and install the trays into the
autosampler tray compartment (see “Installing the Sample Trays” on page 27).
The tray and vial positions from left to right and front to back of the tray compartment
are A01 to C35.
2. Press the RUN key.

Monitoring the Run Status
Depending on whether you have loaded sample sets into the sample queue, the status
screen displays the following:
• If there are sample sets in the sample queue, the RUN status for the sample queue is
displayed on the Status screen (see Figure 58).
• If the queue is empty, the autosampler prompts you to access the Samples menu so
that you can add sample sets to the queue. After you have added sets, press the RUN
key to start your run.

When you press the RUN key, the autosampler begins processing vials when the temperature
for the column oven, tray compartment, or both reaches the set point; the equilibration delay
time (entered in the More menu) has elapsed; and the tray compartment door is closed. If the
autosampler is connected to an LC pump through a contact closure connection, the
autosampler also waits until the pump is ready.
During the run, the Status screen appears (see Figure 58).
Note You can change the ready requirements by choosing Options > Ready Participation
and selecting Enable or Disable in each field. See “Ready Participation” on page 48.
Figure 58. Status screen
Sample queue status
Injection status
Injection status
Temperature status
The Status screen gives you four kinds of information (from top to bottom):
• “Sample Queue Information” on page 83
• “Injection Status” on page 84s
• “File Status” on page 85
• “Temperature Status” on page 85

Sample Queue Information

Information on the sample queue is presented in the first two lines of the Status screen
(see Table 14).
Table 14. Sample queue status fields
Field Description
QStatus Displays the status of the queue (IDLE, PAUSE, RUN, EQUIL, ABORT).
Message Meaning
IDLE Indicates that no sample sets are currently being processed in the queue.
Tip The IDLE status does not indicate if sets are loaded into the queue. To check the contents of
the sample queue, press the MENU key and select QUEUE.
PAUSE Indicates that a sample set is loaded, but that processing has been suspended. If you
pause the queue (by pressing the STOP key once), you can either resume processing
with the current or subsequent vial, or cancel processing of the current sample set
(see “Stopping a Run” on page 88).
RUN Indicates that a sample set in the queue is being processed.
EQUIL Indicates that the autosampler is waiting for the equilibration delay (temperature
zone and initial conditions) to be reached before it starts processing the current
sample set. This status is displayed until the oven and tray compartment reach their
set temperatures, the equilibration time has elapsed, or both.
ABORT Indicates that the processing of the current sample set has been stopped (by pressing
the STOP key and selecting ABORT from the Abort/Continue menu) or that a
system error has occurred. The QStatus displays ABORT until the autosampler has
returned the active vial to the sample tray and flushed all the lines. For more
information about Abort, Continue, and Pause, see “Stopping a Run” on page 88.
Set Displays the number of the sample set currently being processed (1 to 39, P). If the queue is not
running (the QStatus reads other than RUN or PAUSE), the set field is blank.
#Samples Displays the number of the sample currently being processed and the total number of samples in the
set: current sample number/total of samples. For example, if the autosampler is processing sample 50
in a set of 120 samples, the #Samples field reads 50 / 120.
Tip The total does not indicate the total number of vials or the total number of injections in the
set. Calibration vials are not included.

Injection Status
After you start a run, pressing the DOWN ARROW key ( ) displays the injection status
screen that contains information on the injection in progress (see Table 15).
Tip The Status Screen updates every two seconds.
Table 15. Injection status parameters (Sheet 1 of 2)

Field Description
Status Displays the progress of the current injection. A time in minutes in the Status field indicates
that the queue is running (RUN) and that the current sample has been injected. In addition
to the run time, the status field displays these messages.
Message Meaning
RDY Indicates that the autosampler is ready for an injection (all temperature
zones and gradient conditions have been reached), but that no injection is
currently in progress.
NOTRDY Indicates that the autosampler is not ready for an injection. NOTRDY
might indicate that the temperature zones are not stabilized, the door is
opened, or the Pump Ready contact closure is in the wrong state.
GRAD Indicates that the autosampler is waiting for the set gradient conditions to
be reached—that is, for the gradient delay time set in the More menu to
elapse.
HOLD Indicates that an injection hold is in effect as determined by the Inject
Hold input or as set in the Input Polarity menu.
ABORT Indicates that the current injection has been stopped in one of two ways:
• By pressing the STOP key to stop the Queue and selecting ABORT
from the Abort/Continue menu
–or–
• By an error condition occurring
During the ABORT sequence, the autosampler returns the current vial to
the sample tray and flushes the lines.
DOOR Indicates that the door is open. The autosampler automatically moves the
arm to the home position to provide easy access to the sample tray. The
arm automatically resumes where it left off when the door is closed.
Vial Indicates the position and type of vial (S for sample vial, C for calibration vial) currently
being injected. If no injection is in progress (the Status reads NOTRDY), this field is blank.

Table 15. Injection status parameters (Sheet 2 of 2)

Field Description
Vol Displays the injection volume for the current vial. If the current vial is a sample vial, this
field indicates the Injection Volume value entered in the Injection menu. If the current vial
is a calibration vial, this field displays the Injection Volume value entered in the Calibration
menu.
#Inj Displays a fraction that indicates the current injection number over the total number of
injections requested for the current vial: current injection number/injection per vial. For
example, if the autosampler is performing the third of five injections, the #Inj field reads
3 / 5.
File # Pressing the DOWN ARROW key ( ) displays the number and name of the file assigned
to the sample set currently being processed.
Temperature Status Pressing the DOWN ARROW key ( ) accesses the Temperature Status screen, which
displays the actual temperature of the column oven and the tray compartment. The
temperature is displayed, even if this option is turned off (not set). OFF indicates that an
option is installed but not turned on in the current file's Injection menu as shown in XXX.
Tip To check the set temperature for the oven, you can return to the Edit menu and view
the information for the appropriate file as long as you have not loaded that file into the
Queue. If you want to check any experimental parameters after loading your run file,
make a copy of your file that you can review before loading it.
File Status
After you start a run, press the DOWN ARROW key ( ) two times to display the file status.
The File field displays the number and name of the file assigned to the sample set currently
being processed.
Temperature Status
After you start a run, press the DOWN ARROW key ( ) three times to display the status of
the column oven and tray compartments (see Table 16).
Table 16. Temperature status
Field Description
Oven
ON or OFF OFF indicates that the oven temperature control is turned off.
Temperature Indicates the actual temperature of the column oven compartment.
Tray
On or Off OFF indicates that the tray compartment temperature control is turned off.
Temperature Indicates the actual temperature of the column oven compartment.

Changing the Run in Progress
To check the set temperature of the column oven or tray compartment, you can return to the
Edit menu and view the information for the appropriate file as long as you have not loaded
that file into the Queue. If you want to check any experimental parameters after loading your
run file, make a copy of your file that you can review before loading it.

Once a run has started, use the Samples menu if you want to change the injection volume,
cycle time, calibration interval, or set assignments for the sample set currently in progress.
Figure 59 lists the changeable parameters in bold-face type and indicates when those changes
take effect. With the exception of the Cycle Time and Calib 1(of X) values, changes made
from the Samples menu take effect on the next sample injection. Changes to the Cycle Time
take effect on the current sample injection; changes to the Calib 1(of X) field take effect on
the next recalibration. Samples menu changes remain in effect until the next sample set.
Figure 59. Samples menu
\
Note Changing one vial location does not affect other vial locations.

• “Priority Sample Sets” on page 87
• “Stopping a Run” on page 88

Priority Sample Sets

A priority sample set is one that you can insert into the currently active sample set at any time.
It shares the same file and resources as specified for the currently active set.
Priority sample sets are like other sample sets with several important exceptions:
• You assign their priority set number (P) in the Samples menu (not in the Queue menu).
• You cannot change the order of priority sample sets once they are loaded into the sample
queue.
• If you want to run priority sample sets, you must select Reuse Same Vials as the
calibration routine type. (If you select Intersperse Vials, the autosampler does not
distinguish whether a subsequent vial is a calibration vial or a sample vial. As a result, it
cannot resume the calibration routine after the priority sample set is processed.)
• Since a priority set is inserted into the currently active set, you cannot edit or change the
file between the currently active set and the priority set.
Y To insert a priority sample set into the sample queue
1. Press the Samples key.

2. Press the [+] and [–] keys to change the Set field value to P.
Figure 60 shows a priority sample set with P in the Set field.
Figure 60. Samples menu with a priority sample set
3. Fill in the other file parameters as you would for any other sample set.
4. Add the priority set to the queue.
The autosampler assigns a P (priority) order to the priority set as shown in the Queue
menu (see Figure 61):

Figure 61. Queue menu with one priority sample set
Tip The door is equipped with a safety interlock that automatically moves the
autosampler's arm to the home position to allow you to add samples to the tray during a
run. Once the door is closed, the arm returns to its position and resumes the operation in
progress before the door was opened. If necessary, however, you can disable the door
interlock. Press the MENU key, and then select OPTIONS > Ready Participation. In
the Door Interlock field, press the [+] and [–] keys to select DISABLE.
Stopping a Run
The STOP key has several functions depending on the instrument's status when you press the
STOP key. See Figure 62 for an illustration of the Pause/Stop/Abort sequence.
Figure 62. Queue Stop/Abort sequence
Queue is running.
Press STOP.
(User Abort)
STOP requested
Select ABORT SAMPLE/CONTINUE.
Select ABORT. Select CONTINUE.
Returns vial to tray and flushes lines. Resumes queue

System with current vial.
STATUS goes to ABORT.
Error
Pauses the queue.
Press STOP. Press RUN.
Stops the queue. Resumes queue.

QSTATUS goes to IDLE. with current vial.
Press RUN
Restarts queue from

the beginning.

If the queue is in RUN when you press the STOP key, the autosampler suspends its current
operation until you select ABORT (see Figure 63) or CONTINUE (see Figure 64):
Figure 63. Abort prompt
Figure 64. Continue prompt
If you select Continue (by pressing the [+] key), the autosampler returns the queue to the
ACTIVE state and resumes the motor activity (as if you had not pressed the STOP key).
If you select Abort or if a system error occurs, the autosampler follows this sequence:
1. Cancels the processing of the current sample.
2. Returns the active vial to the vial tray.
3. Flushes the lines.
4. Puts the queue in the PAUSE state (Figure 65).
Figure 65. Queue Status line when the autosampler is in the PAUSE state
When the queue is paused, you can do one of the following:

• Press the RUN key to resume processing of the current vial.
–or–
• Press the STOP key to stop the queue (the QStatus goes to IDLE), and then press the
RUN key to restart processing from the beginning of the queue.
This STOP/Abort sequence gives you several opportunities to stop and resume or restart the
run as needed.
Using the ABORT/CONTINUE selections and QPAUSE states, you can remedy problems
that might adversely influence the processing or data received from the current or subsequent
vials (depleted solvent supply, and so on) and resume the run without loss of previous data.
Using the ABORT selection and the STOP and RUN keys, you can stop the current run and
remedy problems that might have influenced the processing or data received from all prior
injections (incorrect file assigned to the set, incorrect solvent concentration, and so on). This
second option minimizes loss of resources (and valuable time).

File Management
File Management
In addition to learning how to edit and load files from the Files menu, you can also copy and
delete files, protect files from editing, and lock files to prevent changes to the run file during a
run.
Saving Files
As you know, the autosampler automatically saves your file when you exit the Edit menu.
If a power failure occurs while you are editing a file, you lose all current changes. However, if
a power failure occurs after you exit the Edit menu, your changes are saved.
Copying Files
Y To copy a file
1. Press the MENU key, and then select FILES > Copy.
The Copy menu appears (see Figure 66).
Figure 66. Copy menu
2. Enter the number of the file to be copied in the Copy File field.
3. Enter the number of the file you want to copy to in the To field.
4. Press the ENTER key.
The **File Copied** message appears briefly and the application returns you to the Files
menu.
Deleting Files
Deleting a file restores all parameters to their default values.
Y To delete a file
1. Press the MENU key, and then select FILES > Delete.
The Delete menu appears (see Figure 67).
Figure 67. Delete menu

File Management
2. Enter the number of the file you want to delete and press the ENTER key.
The **File Deleted** message appears briefly and the application returns you to the Files
menu.
Protecting Files
You can protect a file from being edited or deleted by using the file protection feature in the
OPTIONS menu. Because this feature enables you to control the changes to an original run
file, you can easily incorporate your autosampler files into your standard, good laboratory
practice (GLP) protocols.
Y To display the Configurations menu
Press the MENU key, and then select OPTIONS > Configurations.
The Configurations menu appears (see Figure 68).
Protected file
Y To protect a file
1. Move the cursor down to the Protect field in the line that contains the file you want
secured.
2. Press the [+] and [–] keys to turn the protect function to On.
For example, you cannot edit the Vitamins file shown in Figure 68 until you turn the
protect function off. Attempting to edit a protected file displays the following message:

Optimization
Changes to Real-Time Editing

If a file is protected, you cannot change the injection volume, number of injections per vial, or
cycle time for the run in progress, and these lines are absent from the Samples menu as shown
in Figure 69.
Figure 69. Samples menu for a protected file
Optimization
This section describes how to select the sample loop and syringe size to obtain maximum
reproducibility when performing large-volume injections, how to adjust the draw speed for
viscous samples, and how to adjust the needle height for sample vials containing either a
limited sample volume or precipitates.

• “Injection Volume” on this page
• “Solvent Viscosity” on page 94
• “Needle Height” on page 95
Injection Volume
The maximum injection volume depends on these conditions:
• The volume of the syringe currently installed as designated under
OPTION > Configuration > Syringe Size
• The Injection Type selected under FILE > More > Injection Type
• The volume of the installed sample loop
By changing the sample syringe, the sample loop, or both, you can set up your autosampler to
deliver injection volumes larger than can be delivered by the 250 μL syringe shipped with the
instrument.

Optimization
Y To prepare your instrument for large-volume injections
1. Determine the correct sample loop size for the injection volume desired. See Table 17.
2. Use the injection volume and algorithms outlined below to determine the required
syringe size.
These algorithms define the amount of sample needed for your injection volume:
PushLoop Injection Volume + 15 μL

Pull Loop Injection Volume + 1.1 μL
Full Loop Injection Volume × 1.33 + 70 μL
3. Change your sample loop and syringe. (For instructions, see “Changing the Sample
Loop” on page 121.)
4. Enter the syringe size in the FILE > Configuration > Syringe Size field.
5. Enter the Injection Type in the OPTIONS > More > Injection Type field.
6. Enter your injection volume in the Injection menu.
Tip If you select the Full-loop type, the maximum value depends only on the loop
size, assuming that the syringe size is larger than the loop size. (Loops come only in
the sizes listed in Chapter 8, “Replaceable Parts.” )
IMPORTANT For pull-loop and PushLoop injection, to ensure maximum

reproducibility, do not inject more than half of the sample loop volume.
Table 17. Recommended injection size for selected sample loop sizes*
Injection volume (in μL)
Injection type
Sample loop size (μL) PushLoop Pull Full
5 2.5 2.5 5
10 5.0 5 10
20 10 10 20
50 25 25 50
100 50 50 100
200 100 100 200
500 200 250 500
1000 200 500 1000
* These recommended volumes provide the best chromatographic performance. The type of system being used
determines the maximum injection sizes.

Optimization
The syringe size needed will be the total volume determined by these algorithms. For
example, for a 500 μL full-loop injection (using a 1000 μL loop), the total volume (TV)
needed is as follows:
TV = 500 μL × 1.33 + 70 μL
TV = 735 μL
You would then need a 1000 μL syringe, as there are no 735 μL syringes available. See
Table 18.
.
Table 18. Maximum injection size for syringe size

Syringe size (in μL)
Injection type 250 500 1000 2500 5000
Push Hi 200 200 200 200 200
Pull 212 461 956 1500 1500
Full 100 200 500 1000 1000
Solvent Viscosity
You can adjust the syringe speed (draw rate) for your solvent viscosity from the Solv Viscosity
field in the Configurations menu (see Figure 70).
Sample Syringe Size 250
---------------------------------------------------------
Prep Installed No
Oven Installed Yes
Tray Temp Installed No
File Protect
1: Off
2: Off
3: Off
4: Off
Solv Viscosity Normal Solvent viscosity
menu item
Using the [+] and [–] keys, you can select from three different syringe speeds:
• Normal (fastest)
• Medium
• Viscous (slowest)

Optimization
Use Normal to optimize your cycle time; Normal is optimal for most applications. With very
viscous solvents or normal-phase (low viscosity) solvents, you might want to use the Viscous
setting to slow down the syringe rate. This will prevent cavitation and nonreproducible
injection volumes.
Needle Height
For some applications, such as liquid-liquid extractions and low-injection volumes, you might
need to change or optimize the needle height. On the SpectraSYSTEM autosampler, the
needle does not move. Instead, the bottom of the vial moves relative to the needle tip. The
needle height is the approximate distance between the needle tip and the bottom of the vial
(0 to 20 mm).
The default setting of 2 mm in the More menu is sufficient for most applications and
accommodates a wide variety of vials (see Figure 71). However, cases where you have very
limited sample volumes might require further optimization.
Note The thickness of the bottom of the vial varies considerably between vial types
(1.8 mL vials, microvials, and vials with micro-inserts, and so on) and materials, such as
glass or plastic.
Figure 71. Needle Height field in the More menu
IMPORTANT Operating the autosampler with a needle height that is different from the
default height might bend the needle. Do not adjust the needle height without a spare
needle available.
Y To optimize the needle height for your sample vials
1. Fill a vial with 200 to 300 μL of water and place the vial in position A01.
2. Create an autosampler file that makes two 200 μL injections.
a. In the Injection menu, set the Injection Volume field to 200.
b. Set Injections/Sample to 2.
3. Run the file and observe the amount of fluid remaining in the vial. The fluid height
indicates the position of the needle tip from the vial's bottom.
4. In the More menu, adjust the Needle Height value until the needle tip is located
approximately 1 to 2 mm from the bottom of the vial.
5. Repeat steps 1 to 3 to confirm the needle height is 1 to 2 mm from the vial bottom.

Special Commands in the Commands Menu

The autosampler has several built-in commands for manually manipulating some of the
autosampler's components (the arm, injection valve, and so on) outside of a run. These
commands are useful during maintenance and troubleshooting procedures and are accessible
from the Commands menu (see Figure 72).
Figure 72. Commands menu
Flush Sample Syringe
Initialize Hardware
Injector
Arm
These topics describe the commands available from the Commands menu:
• “Flush Sample Syringe” on this page
• “Initialize Hardware” on page 97
• “Injector” on page 97
• “Arm” on page 97

Use this command to manually flush the 250 μL sample syringe. You used this command
when you primed your autosampler, but you can also use it for maintenance and
troubleshooting.
Y To access the flush sample syringe test
1. Fill your flush solvent bottle, if you have not already done so.
2. Press the MENU key, and then select COMMANDS (see Figure 72).
3. Select Flush Sample Syringe.
The Flush command appears (see Figure 73).
4. Press the [+] and [–] keys to select the desired flush volume in microliters. Then press the
ENTER key to initiate the flush operation.
Figure 73. Flush command
The autosampler automatically flushes the sample syringe and flush lines with the specified
volume of flush solvent and returns the syringe to its starting position. During the flush
sequence a confirmation message is displayed.

Initialize Hardware
Use the Initialize Hardware command to manually control the autosampler's syringe and
injection valve. This command brings the syringe to the initial position and removes any
backlash.
Injector
Use the Injector command to manually switch the injection valve between the inject and fill
positions. Selecting Injector displays the menu shown in Figure 74.
Figure 74. Injector command
Pressing the [+] or [–] key and then pressing the ENTER key changes the injection valve's
position.
Arm
The Arm menu contains a routine for returning the XYZ arm to its home position and a
routine for aligning the arm. Figure 75 shows the Arm menu.
Figure 75. Arm menu

Home Arm
Pressing the ENTER key with the cursor in the Home Arm field moves the arm from its
present position to its home location (the left side in the back-left corner of the tub). See
Figure 76.
Figure 76. Autosampler arm in the home position
Autosampler arm in
the home position
A
B
C
Align Arm
The Align Arm routine moves the arm to the vial position requested. It is used primarily by
Thermo Fisher Scientific field service engineers to properly adjust the arm's x-y-z reference
points. If you suspect that the arm's alignment is incorrect, call your Thermo Fisher Scientific
service representative.
Figure 77. Align Arm command

5
Diagnostic Procedures
This chapter describes the built-in diagnostics and how to determine the gradient delay
volume of your LC system.
Contents
• Gradient Delay
• Diagnostics in the Tests Menu
Gradient Delay
Gradient delay is a user-defined value that delays the injection of a sample. This delay is the
amount of time required for a change in the mobile phase to travel from the gradient
proportioning valve to the injection valve. The volume of mobile phase contained between
the two valves is also referred to as the precolumn volume (PV).
Although not required for normal autosampler operation, Thermo Fisher Scientific
recommends adding a gradient delay value to your Edit file when using large volume
pre-filters or low flow rates (<0.5 mL/min).
Y To add the gradient delay time for your LC system to your Edit file
1. From the main menu, select FILES > Edit.

2. Open your autosampler file.
3. Press the DOWN ARROW key ( ) until you reach the More menu, and then press
Enter.
4. In the More menu, press the DOWN ARROW key ( ) until you reach the Gradient
Delay field.

5 Diagnostic Procedures
Gradient Delay
Figure 78. More menu
5. Press the [+] or [–] key to enter the gradient delay time for your LC system in minutes.
The range is 0.00 to 99.99 minutes.
Calculating the Gradient Delay Time

Y To calculate the gradient delay time for your HPLC system
1. Inject an unretained sample into your LC system with a column inline and using 100% A
as the mobile phase (for example, MeOH).
2. Change to 100% B (for example, 0.1% acetone in MeOH) as fast as possible
(0.1 minutes for SpectraSYSTEM pumps).
3. Subtract the retention time (RT) of the unretained peak from the retention time of the
start of the baseline shift (T2 – T1).
4. Subtract the time required to switch solvents from 100% A to 100% B.
The resulting time is the gradient delay time.
Gradient Delay Example

The following example illustrates how to determine the gradient delay volume for your LC
system.
An unretained peak has a retention time of 3.0 min with a baseline shift at 4.5 min and a
complete mobile-phase switch time of 0.1 min (see Figure 79). The gradient delay is
calculated as follows:
Gradient Delay = (T2 – T1) – 0.1 min
= (4.5 – 3.0) – 0.1
= 1.4 min

Diagnostics in the Tests Menu
Figure 79. Chromatographic results for a gradient delay time experiment

Pump to detector
Injection valve Pump to

to detector injection valve
Baseline
shift
Unretained
peak
Inject T1 T2
Time (in minutes)

The SpectraSYSTEM autosampler has built-in diagnostic routines accessible from the
Tests menu. Using these tests, you can access the operation of your autosampler. In addition
to describing each of these tests, this section shows how the diagnostic tests are run and how
to interpret the error screen information when a test fails.
All of the test screens are arranged similarly. You initiate a test by pressing the ENTER key.
While a test is in progress, the name of the test is displayed along with three dots (Figure 80).
Figure 80. Test in-progress screen

Interpreting the Results

When the test is complete, either a PASS or FAIL result is displayed. When a test fails, an
error screen similar to that shown in Figure 81 appears with the following information
(described in Table 19):
• Test identification
• Fault code (diagnostic error)
• Module identification
• [RUN] / [STOP]
Figure 81. Error screen for a diagnostic test
Test Fault code
Module
Note The error number in this screen is just an example to show you the screen layout.
Table 19. Error screen fields from top left

Field Description
Test identification The name of the test being run.
Fault code The error number associated with the specific failed result. To
receive further assistance in diagnosing and solving the problem,
document and report the fault code to your service
representative.
Module identification Displays the specific autosampler board or assembly where the
problem occurred.
[RUN / STOP] Prompts you to press the RUN key to repeat the test or to press
the STOP key to exit the current test and return to the Tests
menu.

Test Descriptions
All diagnostics and built-in assessment routines are accessible from the Tests menu
(Figure 82). This topic describes the items in the Tests menu.
Figure 82. Tests menu
Software Version
Display Input States
Display Output States
Display Timed Events
RAM Test
ROM Test
Hardware Test
Test External Contacts
Test Comm Port
Initialize EEPROM
Software Version
Selecting this field displays the current software version number, x.yy.zz.
Display Input States

This menu (Figure 83) shows the current states of the TTL-input device signals (Hi or Lo).
You can use this information to check the level of the Pump Ready and Injection Hold input
lines from other LC system modules. You can also diagnose situations where the autosampler
is waiting for ready or waiting to inject. Make sure the Input Polarity is set to the proper level
for each of these signals. Pressing the UP or DOWN ARROW key ( or ) returns you to
the Display Input States field in the Test menu if you want to repeat the test.
Tip You can change the active polarity of a specific input signal from the
OPTIONS > Input Polarity menu.
Figure 83. Display Inputs States menu
Display Output States

This menu shows the current states of the TTL-output device signals (Hi or Lo). Use this
information when hardwiring your autosampler to other LC system modules. Pressing the UP
or DOWN ARROW key ( or ) returns you to the Display Output States field in the
Test menu if you want to repeat the test.
Tip You can change the active polarity of a specific input signal from the
OPTIONS > Input Polarity menu. This menu shows the states of the TTL output device
signals (Hi or Lo) as shown in Figure 84.

Figure 84. Display Output States menu

This menu (Figure 85) displays the current states of the timed events outputs. Use this
information when hardwiring your autosampler to other LC system modules. For more
information, see “General Chromatography Troubleshooting” on page 129.
Figure 85. Display Timed Events menu
RAM Test
This test (Figure 86) writes to and then reads the contents of the random access memory. If
the write information is the same as the read information, the test is successful. You might
want to run this test once a month to verify proper software operation.
Figure 86. RAM Test menu
If the test is successful, the autosampler returns a PASS result (Figure 87). If unsuccessful, the
autosampler returns a FAIL result and displays an error message. Document the test results
and error message, and call your Thermo Fisher Scientific service representative.
Figure 87. Successful RAM Test
Press the STOP key to return to the Tests menu.
ROM Test
This test evaluates check-sums on the contents of the instrument's ROM and compares the
results to known values.
If the test is successful, the autosampler returns a PASS result. If unsuccessful, the autosampler
displays the number of the failed chip or chips, along with the regular error screen
information (Figure 88). If the test fails, document the test results and call your Thermo
Fisher Scientific service representative.
Figure 88. Failed ROM Test

Hardware Test
The hardware test is the most important autosampler diagnostic. It checks all of the cable
connections, sensors, motors, circuitry, and attached components.
Before running this test, be sure that the XYZ arm is in the home position (at the left back of
the sample compartment), or the AS3000 autosampler might report false errors. You can use
the Home Arm command in the Commands menu (see “Special Commands in the
Commands Menu” on page 96) if the arm is not in the home position.
If the Hardware Test fails, the screen displays the test identification, fault code, applicable
module or connection, and [RUN] / STOP] fields. For example, in Figure 89, the message
J10/J40/J45 indicates that further troubleshooting is required. Document the screen
information and report it to your Thermo Fisher Scientific service representative when you
call for assistance.
Figure 89. Example error screen
Pressing the STOP key returns you to the Tests menu.
Most of the failed Hardware Test results require that you contact your service representative
for assistance. However, two of the messages indicate problems that you can likely resolve
without a service call.
• Opt Config
This message indicates an incorrect configuration. Check the Configurations menu
(under OPTIONS) and verify that the options field entries match your installed options.
• Arm,*
This message indicates that the XYZ arm was not in its home position when the
Hardware Test was initiated. Select COMMANDS > Arm > Home arm.

This test activates all of the external contacts and tests for proper activation. Do not run the
test while the external contacts are wired to other equipment, or the test will report false
errors. Before running this test, disconnect the 12-pin connector block from the back of the
instrument. After the test is complete, plug the connector back in to resume normal
instrument operation.
Pressing the ENTER key with the cursor in the Test External Contacts field displays a
warning prompt (Figure 90).
Figure 90. External Devices menu

From this menu, you can use the [+] and [–] keys to select CONTINUE or ABORT.
Selecting Continue starts the test.
Selecting ABORT discontinues the test and returns you to the Test External Contacts field of
the Tests menu. If ABORT is displayed and you want to resume the test, press the LEFT or
RIGHT ARROW key. The display changes from ABORT to CONTINUE.
Test COMM Port

Use this test to assess the operation of the communications port on the autosampler’s back
panel. This test sends a signal to the communications port and expects a signal in return. A
successful result is reported as a PASS; an unsuccessful result is indicated by the regular error
screen.
To perform this test, you must connect a loop-back connector to the communications port.
Tip If you want to perform this test, contact your Thermo Fisher Scientific field service
engineer for the procedure and the necessary parts information.
Initialize EEPROM
The Electronically Erasable Programmable Read Only Memory (EEPROM) stores all files,
user-set variable values, and system configuration information when the power is turned off.
Reinitializing the EEPROM restores the default values to all files and erases the system
configuration information. Pressing the ENTER key in this field displays the message shown
in Figure 91.
Figure 91. Initialize EEPROM menu
If you want to exit this routine before running it, you can do any of the following:
• Press the [+] and [–] keys to select No.
• Press the MENU key to open the main menu.
• Press the STATUS key to open the Status Screen.

6
Maintenance
This chapter contains the maintenance schedule and procedures for your autosampler.
Contents
• Specific Hazards
• Maintenance Schedule
• Maintenance Procedures
• Automated Shutdown in the Stand Alone Mode
• Maintenance Log
Specific Hazards
For your own safety and to protect the autosampler from damage, follow the safety
precautions in this manual when performing maintenance on the autosampler.
CAUTION Alerts you to situations that could result in personal injury and tells you how to
avoid them.
CAUTION High Voltage. Alerts you to the presence of high voltage and to the potential
injury that could occur from electrical shock if you came into contact with a specific
instrument area or component. Also indicates how to avoid contact with the high-voltage
areas in your instrument.
CAUTION Hot Surface. Alerts you to potential injury that could occur from contact
with a heated surface or area on or in an instrument. Also indicates how to avoid contact
with the heated surfaces in your instrument.

6 Maintenance
Maintenance Schedule
Maintenance Schedule
Your autosampler requires only a few simple maintenance procedures to keep it in optimal
working condition. Table 20 contains the maintenance schedule for the autosampler. Ensure
that only a Thermo Fisher Scientific service representative or other qualified person performs
the yearly maintenance tasks.
CAUTION To avoid electrical shock, do not remove the top cover or remove parts beyond
the descriptions in the operation portions or in the maintenance topics of this manual.
Table 20. Maintenance schedule

Frequency Task Performed by
Daily Empty flush-solvent tray. User
Monthly Inspect the sample needle module. User
Check the solvent tubing and connections for leaks. User
Clean the drop catch. User
Semi-annually Replace the flush-solvent inlet filter. User
Replace the needle assembly. User
Annually or as Replace the injection valve's rotor seal. User
necessary
Clean and lubricate the syringe drive mechanism. Service
Clean and lubricate the XYZ arm. Service
Verify the XYZ arm alignment. Service
IMPORTANT You are responsible for maintenance of the autosampler. Routine

maintenance is not provided under warranty; however, planned maintenance contracts are
generally available. If you are interested in purchasing a planned maintenance contract,
contact your local service representative.
This chapter contains recommended maintenance intervals based on operating the

autosampler under typical conditions. Operating the autosampler under certain harsh
conditions (corrosive solvents, extreme temperatures, and so on) might require more frequent
maintenance than indicated in this chapter.

6 Maintenance
Maintenance Procedures
This section contains the following maintenance procedures:
• “Emptying the Flush-Solvent Tray” on this page
• “Replacing the Rotor Seal” beginning on this page
• “Replacing the Flush Solvent Inlet Filter” on page 115
• “Maintaining the Sample Needle Module” on page 115
• “Replacing the Syringe” on page 118
• “Changing the Sample Loop” on page 121
• “Replacing the Fuses” on page 122
Emptying the Flush-Solvent Tray

For normal operation, you might need to empty the tray at least once or twice a day.
Y To empty the flush-solvent tray
1. Be sure the autosampler is in IDLE status.

2. Carefully slide the tray out without spilling the collected solvent.
3. Empty the tray, rinse it off with water, and slide it back into place under the elbowed,
barbed piece of black tubing.
CAUTION Wear skin and eye protection and dispose of hazardous waste according to
local, state, and federal regulations.
IMPORTANT Be sure that the level of the liquid in the waste container is below the level
of the instrument, or waste will collect in the lines and can backflush into the instrument.
Replacing the Rotor Seal

To replace the rotor seal, follow these procedures in order:
1. Removing the Injection Valve
2. Disassembling the Injection Valve
3. Cleaning the Stator
4. Installing the Rotor Seal
5. Reinstalling the Injection Valve

6 Maintenance
Removing the Injection Valve

If you are only replacing the rotor seal, you do not have to remove the injection valve from the
instrument; however, it is easier if you do. If you want to replace the rotor seal with the valve
installed, proceed to the section entitled, “Disassembling the Injection Valve” on page 111.
Y To remove the injection valve from the autosampler
1. Using a 1/4 in. open-end wrench, disconnect the tubing from ports 2, 3, 5, and 6 of the
injection valve (see Figure 92).
2. Remove the sample loop.
3. If your autosampler has a column oven, loosen and remove the two Phillips-head screws
that secure the injection valve collar to the front of the oven. Then remove the collar.
4. Remove the two Phillips screws that secure the valve mounting plate.
5. Carefully pull the injection valve out of the instrument.
Figure 92. Injection valve tubing connections
2 Needle tubing
3 1 Flush tubing
4 6
5
RUN STATUS MENU
STOP
ENTER
SAMPLES SpectraSYSTEM AS3000
WARNING
Connect to the
Return from the left side of the
heat exchanger dead volume union

6 Maintenance
Disassembling the Injection Valve

To replace the rotor seal, disassemble the injection valve on a clean benchtop.
IMPORTANT Do this repair in a clean environment. Component cleanliness affects the

useful life of your injection valve.
IMPORTANT Do not activate the valve mechanism with the injection valve removed from
the instrument or risk damaging the valve mechanism.
Y To disassemble the injection valve
1. Remove the injection valve from the autosampler (see “Removing the Injection Valve” on
page 110).
2. Using an Allen wrench, remove the 9/64 in. hex cap screws from the top of the valve
(Figure 93).
3. Carefully lift the stator from the valve body and set it onto a clean surface.
Figure 93. Injection valve components
Valve Rotor Hex cap
base seal screws
Valve Valve Stator

shaft body
Note Be careful not to drop the two rotation stop pins that protrude from the valve
base (Figure 94).
4. Remove the valve body.

5. Before removing the worn rotor seal, note these details on the rotor seal (Figure 94):
• The three circular port grooves on one side of the rotor (the other side is smooth)
• The small locating notch on the rotor's rim (not the V stamped on the seal)
Figure 94 shows the injection valve with the valve body removed and the rotor seal
exposed. The valve’s mounting bracket is not shown.

6 Maintenance
Figure 94. Injection valve with valve body removed and rotor seal exposed
Three circular port grooves

Rotor seal
Notch
Horizontal locking pin
Valve body
Valve base
Vertical stop pins
6. Remove the worn rotor seal. You might need a thin, flat-bladed tool to remove the seal.
Cleaning the Stator

Determine whether the stator requires cleaning by inspecting it.
Y To clean the stator
1. If it is dirty or greasy, swab the stator with HPLC-grade methanol. If more stringent
cleaning is required, use a sonicator.
2. Inspect the remaining valve components for contamination. Clean as necessary.
IMPORTANT If the stator is scratched, replace it. Scratches can damage the rotor seal and
cause valve leaks.
Installing the Rotor Seal
Y To install the rotor seal
1. Install the new rotor seal in exactly the same orientation as the old one. Be sure that the
rim notch is in line with the horizontal locating pin and that the circular port grooves are
visible.
2. Install the valve body.

6 Maintenance
3. Install the stator onto the valve body carefully, observing that the two locating pins in the
valve body (Figure 94) line up with the two holes on the bottom side of the stator
assembly (Figure 95).
IMPORTANT Be sure to hold the valve shaft so that the horizontal locating pin
touches the left stop pin as you reassemble the valve. This puts the valve into the
INJECT position (the same position as when you removed the valve from the
instrument). If the pins are not in the correct orientation, the valve shaft might not be
in the proper orientation for reinsertion into the instrument.
Figure 95. Bottom of the stator assembly

Locating hole
Screw hole (3X)
Stator face
Setscrew (3X)
Locating hole
IMPORTANT These locating pins orient the stator assembly in one of two positions,
but only one position aligns the mounting holes in the valve body with the screw
holes in the stator.
4. Insert the three cap screws so that each one just contacts the stator.
IMPORTANT To maintain the necessary pressure for proper valve operation and to
avoid valve binding, look for a uniform gap between the stator and the valve body. Do
not over-tighten the valve.
5. Tighten each cap screw an equal amount until all setscrews are in equal contact with the
valve body.

6 Maintenance
Reinstalling the Injection Valve

If you removed the injection valve from the autosampler to replace the rotor seal, reinstall the
injection valve.
Y To install the injection valve
1. Align the valve shaft with the port for the injection valve.
2. Secure the valve mounting plate with the two Phillips screws.
Figure 96 shows the correct orientation for the valve mounting plate. The locating hole is
below and to the right of the injection valve.
Note When reinstalling the mounting plate and valve assembly, be sure to orient the
bracket with the corner that has the locating hole in the lower right as shown in
Figure 96. Be sure that you can see the pin through the locating hole.
Figure 96. Valve mounting plate in the correct orientation
Mounting plate
Mounting screw
Locating hole
Mounting screw
3. Reconnect the sample loop to ports 1 and 4 of the injection valve.

4. Reconnect the tubing to ports 2, 3, 5, and 6 of the injection valve. Connect the needle
tubing to port 2, the flush tubing to port 3, the dead volume union to port 5, and the
return tubing from the heat exchanger to port 6. Using a 1/4 in. open-end wrench,
tighten the fittings.

6 Maintenance
Replacing the Flush Solvent Inlet Filter

Properly filtering your flush solvent extends the life of your injection valve and column.
Y To replace the inlet filter
1. Be sure the autosampler is in the IDLE mode.

2. Remove the flush-solvent bottle cap and lift out the inlet tubing.
IMPORTANT Be sure to follow all of the safety precautions for each solvent as
prescribed by the manufacturer's MSDS.
3. Put on a new filter cartridge and put the line back into the bottle. Tighten the solvent cap.
4. Flush the inlet filter and lines with an appropriate volume of solvent (~5 μL).
Maintaining the Sample Needle Module

To remove or clean the sample needle module and flush the drop catch, follow these
procedures:
• “Removing or Cleaning the Sample Needle Module” on this page
• “Flushing the Drop Catch” on page 118
Removing or Cleaning the Sample Needle Module

The sample needle module resides in the sample tower and is responsible for piercing the vial
septum and removing sample from the vial. The needle guide end of the module snaps out of
the needle mount. The tubing portion of the assembly is routed through a hole in the column
oven compartment and is connected to port 2 of the injection valve.
Figure 97 shows the sample needle module. Thermo Fisher Scientific supplies two versions of
this module: a standard version and a biocompatible version. If your autosampler has a
biocompatible injection valve, order the biocompatible version.

6 Maintenance
Figure 97. Sample needle module

Needle guide that snaps
into the needle mount
Fitting that connects to port 2
of the injection valve
Standard
SIDE
THIS
OUT
fitting
–or–
Biocompatible
fitting for the
biocompatible
injection valve
Y To remove the sample needle module
1. Using a 1/4 inch open-end wrench, remove the tubing fitting from port 2 of the injection
valve.
2. Carefully (to avoid damage to the tubing) release the sample needle module from the
tower by grasping the module edges and pulling toward the back of the autosampler.
3. Pass the needle fitting through the autosampler's front bulkhead and remove the needle
module from the autosampler.
Tip If you are replacing (not inspecting) the needle, you might want to cut the used
needle to make it easier to pass the fitting through the bulkhead.

6 Maintenance
Figure 98. Sample needle module pulled away from the needle mount
Sample Needle
tub module
assembly
Needle
Front bulkhead
T H IS
S IDE Drop-catch
OUT
location
Injection
tower
Y To clean the sample needle module
1. Inspect the needle module.

2. Rinse in water or sonicate if contamination is present.
3. If internal plugging is suspected, pass a cleaning wire through the needle and flush the
needle with high flow from an LC pump.
IMPORTANT The sample needle module is glued during manufacture and cannot be
disassembled.

6 Maintenance
Y To replace the sample needle module
1. Remove the new module from the replacement kit.

2. Pass the valve end of the needle through the hole on the underside of the column
compartment.
3. Snap the needle assembly into the mounting brackets on the backside of the sample tower
(Figure 98).
4. Place the tube fitting and ferrule onto the needle and install it into port 2 of the injection
valve (Figure 92).
Flushing the Drop Catch

The drop catch (Figure 98) removes the last drop of sample from the end of the needle after
injection. Flush it monthly.
Y To flush the drop catch
1. Remove the needle module assembly as described on page 116, but leave the drop catch
installed.
2. Flush the drop catch with water, an organic solvent, or an acid or base (as appropriate for
the sample), and once more with water. Then dry it with a clean tissue.
Replacing the Syringe

This topic describes how to replace the sample (250 μL) syringe (see Figure 99). You can
replace the 250 μL sample syringe without removing the syringe drive assembly, but you must
move the syringe drive about two inches out by interrupting a flush cycle.
Figure 99. Syringe
Syringe nut Silver base
Metal tip

6 Maintenance
Y To remove the sample syringe
1. From the main menu, select Commands > Arm > Align Arm. Press ENTER.
The autosampler arm moves to position A01at the front left of the tray compartment.
2. From the main menu, select Commands > Flush Sample Syringe.
3. When the plunger is lowered, turn off the power.
4. Hold the silver base of the plunger to prevent it from turning, and loosen the knurled
syringe set screw under the syringe's plunger.
Tip You might need to use a needle nose pliers to loosen the set screw.
Note The syringe set screw is a captive fitting and will not fall into the instrument's
chassis.
5. To loosen the top of the syringe, hold the metal tip on the top of the syringe barrel,
unscrew the used syringe barrel, and lift it out of the instrument.
IMPORTANT Do not try to loosen the syringe by holding the barrel. The syringe
could break between the glass barrel and the metal tip.
Tip Push up on the syringe plunger while lifting it out of place.
Tip Install the syringe in its fully expelled position to prevent an air bubble in the
syringe barrel.

6 Maintenance
Y To install the new syringe
1. Slide the syringe onto the syringe drive assembly (see Figure 100).
Figure 100. Syringe drive assembly with syringe
Syringe valve
Knurled syringe set screw
2. Screw the syringe nut into the syringe valve.

3. Screw the syringe drive assembly nut into the silver base of the syringe plunger.
4. Turn the autosampler on.
Because the arm is not in the home position, an error condition occurs (#140) as the
autosampler goes through its initialization process.
5. Press RUN to clear the error.
Tip If you change the syringe size, do one of the following:

• If you are using the autosampler in the Stand Alone mode, change the syringe size in
the Options > Configurations > Sample Syringe field.
• If you are using a chromatography data system to control the autosampler, enter the
syringe size when specifying the configuration settings for the autosampler.

6 Maintenance
Changing the Sample Loop

A number of different size sample loops are available for the SpectraSYSTEM autosampler.
For the list of spare parts and consumables, see Chapter 8, “Replaceable Parts.”
Y To change the sample loop
1. Be sure that the autosampler is in the IDLE mode.

2. Using a open-end wrench, loosen the fittings at ports 1 and 4, and pull out the two ends
of the sample loop.
3. Insert the ends of the new sample loop in the same orientation as the old one and tighten
the fittings.
Tip If you are using the autosampler in the Stand Alone mode, enter the nominal sample
loop size in the File > Injections > Loop Size field when making full-loop injections.
If you are using a chromatography data system to control the autosampler, enter the
sample loop size when specifying the configuration settings for the autosampler.

6 Maintenance
Replacing the Fuses

Instrument power is supplied by two time-lag fuses housed in the fuse compartment on the
lower left of the instrument's back panel (Figure 101).
Figure 101. Autosampler’s back panel
12
11
10
9
8
7
6
5
4
3
2
WARNING 1

C
O
M
M
ATTENTION
indispensable avant
WARNUNG
11.
Description
TIMED EVENT 1
TIMED EVENT 2
Signal
OUT
OUT
8.
TIMED EVENT 4
A/S READY
OUT
OUT
OVEN-TEMP/COOLER 7.
6.
INJ HOLD
INJ OUT
IN
OUT
5. PUMP READY IN
4. GRAD START OUT
3. PUMP STOP OUT
2. + 5V 150mA OUT
1. GROUND ----
4,478.095 4,957,009 5,044,428
4,953,075 5,029,065

Serial No: 180000

Assembled in China
Model No: AS 3000

61010 - 1
CAUTION

LINE 100 V 120 V 220 V 240 V 50/60 HZ

Fuse
AC power compartment FOR CONTINUED PROTECTION AGAINST FIRE HAZARD,
LINE 100 V 120 V 220 V 240 V 50/60 HZ

CAUTION Disconnect the power cord before you replace fuses.
Y To replace the fuses
1. Turn off the autosampler by pressing the on/off button on the lower right corner just
below the front panel.
2. Unplug the power cord from the AC power receptacle on the autosampler’s back panel.

6 Maintenance
Automated Shutdown in the Stand Alone Mode
3. Use a flat blade to press down on the plastic tab at the top edge of the fuse compartment
and pull out the fuse holder.
4. Pull both fuses out of the holder and discard. Place the new fuses into the holder with the
metal end visible.
5. Snap the fuse holder back into place.
Automated Shutdown in the Stand Alone Mode

If you are controlling the autosampler in the Stand Alone mode, you can set it to shut down
the system during periods of disuse, for example, after completing an overnight or
over-the-weekend run. The shutdown feature can turn off the autosampler’s controlled
temperature zones, flush the injection system, and send a signal to the pump to stop the pump
flow. Enter the shutdown parameters in the OPTIONS > Shutdown menu (see Figure 102).
Figure 102. Options menu
Figure 103 illustrates the autosampler's Shutdown menu. Table 21 describes the parameters.
Figure 103. Shutdown menu
Delay Time Off

Oven Shutoff Yes
Tray Temp Shutoff Yes
Pump Shutoff Yes
Flush Volume 400
Table 21. Shutdown menu parameters (Sheet 1 of 2)

Delay Time Specifies the desired amount of time that the autosampler is to
wait before initiating the shutdown procedure. When you select
Off, the autosampler performs the shutdown procedure as soon as
the autosampler state returns to IDLE.
Selections: Off, 5, 10, 20, 30, 45, 60, 90, 120, 240, and
480 minutes
Oven Shutoff Selecting Yes causes the autosampler to automatically turn off the
oven after the Shutoff Delay time has elapsed.

6 Maintenance
Maintenance Log
Table 21. Shutdown menu parameters (Sheet 2 of 2)

Note If you are using the Shutdown function with methods that
call for heating and cooling, be sure to allow a long enough delay
time (10 or more minutes) for thermal equilibrium to occur.
Pump Shutoff Selecting Yes causes the autosampler to automatically activate the
Pump Stop output after the Delay Time has elapsed. Turning off
the pump retains your solvent supply and prevents air from being
pumped into the lines should the solvent reservoirs become
depleted.
Flush Volume Flushes the injection system with the specified volume.
Range: 200 to 5000 μL

Default: 400 μL
Maintenance Log
The Maintenance Log menu (see Figure 104), accessible from the OPTIONS menu,
monitors the autosampler maintenance status and counts, and displays the number of
activations for each of the routine maintenance parts listed in the menu.
Note If you are controlling the autosampler in the SpectraNet mode, set up and monitor
the maintenance log from your chromatography data system.
Figure 104. Maintenance Log menu
For information on the Maintenance Log menu items, see these topics:
• “Instrument Maintenance Status” on page 125
• “Total System Cycles Menu” on page 125
• “Injector Valve Menu” on page 125
• “Needle Wear Menu” on page 127
• “Sample Syringe Menu” on page 127

6Maintenance
Maintenance Log
Instrument Maintenance Status

The Maintenance Log menu provides a convenient way to keep track of autosampler
maintenance. When you first access the Maintenance Log menu from the OPTIONS menu,
the Maintenance Required confirmation message appears if instrument maintenance is
required. This message is displayed if any of the #Cycles field values in any of the
Maintenance Log menus is greater than the number of cycles entered in the Due fields. See
the other topics in this section for more information on these fields.
If maintenance is not required, no message appears. Pressing the DOWN ARROW key ( )
clears the confirmation message and returns you to the Maintenance Log menu.
Total System Cycles Menu

The Total System Cycles menu (see Figure 105) displays the total number of instrument
cycles in the #Cycles field. This field value is set to zero at the factory and cannot be reset. The
Note field is a six-character, alphanumeric, user-programmable field.
Y To enter the last service date or other comments
In the Note field, press the [+] or [–] keys.

Figure 105. Total System Cycles menu
User-entered value
for the last service date
Injector Valve Menu

Except for the Total System Cycles menu, all of the Maintenance Log menus are identical to
the Injector Valve menu (see Figure 106 and Table 22). Only the Injector Valve menu then is
described in detail here.
The Maintenance log menus track the usage for the listed autosampler component. When
you replace the component, reset the counter to 0.
Y To reset the counter to 0
1. Press the [+] or [–] keys to select YES.

2. Press ENTER to accept the new setting.
The **Counter Reset** confirmation message appears.

6 Maintenance
Maintenance Log
Figure 106. Injector Valve menu
Table 22. Maintenance Log menu parameters

#Cycles Displays the number of activations of the specific autosampler part since
the last time this field (counter) was reset (0 to 999 999). The #Cycles
value for each of the Maintenance Log menus is included in the menu
descriptions that follow.
Due Specifies a six-character numeric field where you enter the number of
cycles before maintenance is due.
Range: 0 to 999 999
If the #Cycles field value is larger than the Due field value, the
Maintenance Due message appears when you access the Maintenance Log
menu from the Options menu. The default maintenance Due field value is
12 000 (approximately once a year). The default values for the other
Maintenance Log menus are included in the menu descriptions that follow.
Tip The Due field default values for all of the Maintenance Log menus
are estimates only. The actual values appropriate for your instrument
vary with the type of applications and the specific conditions being used
with your LC. If the "Maintenance Required" message is displayed,
strongly consider replacing parts; however, you might want to increase
the Due value and experiment with extending the time before
performing maintenance. Conversely, if instrument performance
indicates, you might want to decrease the Due field value for some of the
Maintenance Log menus.
Tip Similar to the Total System Cycles menu, this is a six-character,
alphanumeric, user-programmable field. Use the [+] or [–] keys to enter
the last service date in this field, but you might also document contact
information or other comments regarding the maintenance of the
specific autosampler part.
Reset #Cycles Pressing the DOWN ARROW key ( ) displays the Reset #Cycles field
used to reset the #Cycles counter for each autosampler part.

6Maintenance
Maintenance Log
Needle Wear Menu

The #Cycles field in this menu is incremented each time the needle pierces a vial. The default
value of the Due field is 10 000, which corresponds to approximately every six months.
Sample Syringe Menu

The #Cycles field displays each full syringe stroke. However, the instrument tracks the actual
distance of linear travel, thus compensating for different injection (stroke) volumes. The
default Due field value for both menus is 24 000, which corresponds to approximately once
a year.

7
Troubleshooting
This chapter provides information to help you troubleshoot possible autosampler problems.
Contents
• General Chromatography Troubleshooting
• Autosampler Troubleshooting
• Display Messages
• Testing for Tubing Restrictions
For additional assistance in troubleshooting a particular problem, contact Thermo Fisher

Scientific Technical Support or your service representative.
General Chromatography Troubleshooting

The first section focuses on general chromatographic problems and is designed to help you
define the particular instrument or condition causing the problem. Once you determine the
cause, use the ordered outline to fix the problem or refer to the troubleshooting guide for the
specific SpectraSYSTEM instrument. Each of these problems can be detected by monitoring
the chromatography running conditions or by observing the chromatogram.
Table 23. General LC troubleshooting (Sheet 1 of 3)
Symptom Cause/Remedy
1. No flow a. Check mobile phase connections.
b. Check for leaks.
c. Refer to the pump troubleshooting guide.
2. High backpressure a. Check flow rate and system/column specifications.
b. Check for tubing or column blockage.
3. Unstable baseline or drift a. System/column not equilibrated; allow more time.
b. Refer to the detector troubleshooting guide.

7 Troubleshooting
General Chromatography Troubleshooting

4. Baseline noise a. Check for air bubbles in system, degas solvents.
b. Check for system/solvent contamination.
d. Refer to the chromatography data system
troubleshooting guide.
5. No peaks a. Check detector and data system connections.
b. Refer to the autosampler troubleshooting guide.
c. Check sample retention with chromatographic
conditions.
6. Contaminating/ghost peaks a. Clean system and column.
7. Poor peak shape a. Check system for leaks.
b. Check fittings and tubing lengths.
c. Check column performance.
d. Refer to the autosampler troubleshooting guide.
e. Refer to the pump troubleshooting guide.
f. Refer to the detector troubleshooting guide.
8. Poor retention time a. Check system for leaks and bubbles.
reproducibility
b. System/column not equilibrated; allow more time.
c. Check column performance.
d. Refer to the pump troubleshooting guide.
e. Refer to the autosampler troubleshooting guide.
f. Refer to the data system troubleshooting guide.
9. Poor peak area a. Check column performance.
reproducibility
c. Refer to the data system troubleshooting guide.
10. Non-integrated or too a. Refer to the integrator or data system
many peaks troubleshooting guide.

7 Troubleshooting
Autosampler Troubleshooting

11. No instrument of device a. Check cable connections.
control
b. Check system configuration.
c. Refer to the individual instrument troubleshooting
guide.
d. Refer to the integrator, ISM, or data system
troubleshooting guide.
For more detailed chromatographic troubleshooting, refer to any HPLC troubleshooting

reference book or call your local sales or service representative.
This section describes autosampler problems that can affect your chromatography and general
autosampler hardware problems.
For information on troubleshooting autosampler problems that can affect your

chromatography, see Table 24. For information on troubleshooting general autosampler
hardware problems, see Table 25.

7 Troubleshooting
Table 24. Autosampler-specific chromatographic problems (Sheet 1 of 3)

Symptom Possible problem Remedy
1. Baseline drift when the a. Lack of thermal stability in the a. Eliminate drafts around the column
injection valve changes column oven compartment, compartment. Wait until the column
from INJECT to FILL detector, or mobile phase oven has reached thermal equilibrium.
If the problem persists, contact your
local Thermo Fisher Scientific service
representative.
2. Shifting retention a. Temperature variations in the lab a. Stabilize temperature.
times
b. Column-heater problems b. Call your Thermo Fisher Scientific
3. Sensitivity changes a. Inconsistent sample injection a. Check for a partially blocked injection
volumes valve and observe the pressure. If the
problem persists, replace the injection
valve (see “Removing the Injection
Valve” on page 110).
b. Leaks between the injection valve b. Tighten/remake fitting.
and the column causing
inconsistent sample-volume
injection
c. Air bubbles aspirated into the lines c. Replenish/prepare fresh sample and
along with sample repeat the injection.
c. Slow down syringe speed.
e. Sample adsorption to the walls of e. Change the mobile phase
the injection valve or sample loop concentration.
f. Sample solvent incompatible with f. Change solvent; use mobile phase if
the mobile phase possible.
g. Sample insoluble in solvent g. Be sure sample solvent has a lower
elution strength than the mobile
phase.
h. Air in syringe/sample lines h. Flush sample lines.

7 Troubleshooting

4. Irregular peak shapes a. The sample volume exceeds the a. Decrease the volume injected or dilute
column's capacity. the sample.
b. The strength of the solvent used b. If appropriate for your application,
to dilute the sample exceeds the ensure that the flush solvent is of the
strength of the initial same composition as the solvent used
mobile phase. to dissolve the sample and that it never
exceeds the solvent strength of the
initial mobile phase.
c. Degradation of sample c. Prepare fresh sample and repeat
components injection.
5. Band broadening a. Fitting problem at the injection a. Inspect for damage, mismatch,
valve (port 5) to column incorrect assembly.
connection
b. Tubing ID too large b. Use 0.010 inch ID tubing.
6. Smaller than expected a. Smaller than expected injection a. Check the syringe size and the syringe
peak heights volume due to incorrect syringe configuration.
configuration
b. Incorrect injection volume b. Check the injection volume value
in the file.
c. Air in lines c. Flush the lines.
d. Misadjusted syringe-drive d. Call your Thermo Fisher Scientific
mechanism service representative.
7. Peaks during a blank a. Sample carryover due to residual a. Insufficient flush volume. Increase
injection (from a sample in the sample loop Injection Volume in Edit menu, add a
previous injection) blank vial between sample vials, or use
a stronger flush solvent.
b. Sample carryover due to b. Check and remake fittings.
incorrectly assembled sample-loop
fittings (adding dead volume that
can contain residual sample)
c. Sample too concentrated c. Dilute sample.
8. No peaks a. Plugged or bent needle a. Clean/replace needle. Tighten fittings
and syringe.
b. Leaking flush valve fitting b. Tighten fitting.
c. Plugged or leaking tubing c. Replace faulty tubing.

7 Troubleshooting

9. Incorrect precision a. Air leak a. Tighten all fittings and repeat the run.
and/or accuracy
b. Worn out syringe b. Replace.
problem on a
sample of known
content-random error
10. Reproducibility of a. Plugged or bent needle a. Clean/replace needle. Tighten fittings
peak areas and syringe.
b. Leaking flush valve fitting b. Tighten fitting.
c. Plugged or leaking tubing c. Replace faulty tubing.
d. Sample viscosity too low or d. Change viscosity setting in the
too high FILE > Edit > More menu.
e. Solvent viscosity too low or e. Change Solv Viscosity setting in the
too high OPTIONS > Configurations menu.

7 Troubleshooting
Table 25. Autosampler hardware problems (Sheet 1 of 4)

Startup
1. Nothing works a. Power cord unplugged or faulty a. Plug in/replace cord.
when instrument is
b. Blown fuse b. Replace fuse.
turned on.
c. Defective power switch, driver, c. Call your local Thermo Fisher
transformer Scientific service representative.
2. Fan is running but a. Display component failure a. Call your local Thermo Fisher
display does not work. Scientific service representative.
3. No response from a. Defective keypad a. Call your Thermo Fisher Scientific
keypad but display service representative.
works.
4. Column oven, tray a. File not loaded a. Load file.
temperature control, or
both do not turn on.
Communications
5. No RS-232-C a. Further troubleshooting required a. Call your Thermo Fisher Scientific
communications. service representative.
6. EEPROM fails to a. EEPROM not initialized a. Reinitialize the EEPROM. If
retain memory. unsuccessful, might be a defective
PCB. Call your Thermo Fisher
Scientific service representative.
7. External devices (timed a. Incorrect configuration settings or a. Check “Communication: SpectraNet
events) do not work. hardware connections or Stand Alone” on page 30 for
configuration settings and hardware
connections.
b. Interface equipment problem b. Refer to the applicable instrument
manuals.
Vials
8. Vial is stuck in tower. a. Bent needle a. Replace needle module (see
“Maintaining the Sample Needle
Module” on page 115.)

7 Troubleshooting

9. Instrument cannot a. Incorrect vial position entered into a. Check Samples menu.
locate vial. Samples menu
b. Sample incorrectly placed in b. Check tray arrangement.
sample tray
c. Arm misaligned c. Home arm. See “Special Commands
in the Commands Menu” on page 96.
d. Arm movement restricted d. Remove restriction and home arm.
10. Vials do not fit in tray. a. Incorrect vials a. Vial diameter should be
0.44 to 47 inches.
11. Broken vials a. Tray not aligned or not seated a. Seat tray completely in tray chamber
properly and pull handle back toward you.
12. Torn septa a. Bent needle a. Replace needle.
Injection valve
13. Injection valve does not a. Slipping injection valve drive a. Call your Thermo Fisher Scientific
switch. service representative.
14. Injection valve a. Loose or faulty sensor cable a. Call your Thermo Fisher Scientific
continues to rotate service representative.
until fault is generated.
15. Injection valve does not a. Excessive torque required for valve a. Call your Thermo Fisher Scientific
rotate to the proper rotation service representative.
position.
16. Motor fails to stop after a. Possible defective sensor a. Call your Thermo Fisher Scientific
syringe is fully service representative.
returned.
17. Sample loop does not a. Blocked injection valve a. To isolate blockage and flush, follow
fill. procedures on “Replacing the Flush
Solvent Inlet Filter” on page 115. Or,
take apart valve and sonicate.
CAUTION Do not clean valve
with a cleaning wire, or you risk
damaging it.
b. Blocked sample loop b. Backflush loop. If problem persists,
replace the loop.
c. Worn syringe c. Substitute a "known-good" syringe
and determine if symptoms persist.
d. Blocked needle d. Clean with a cleaning wire.

7 Troubleshooting

18. Valve-seal wears a. Too much valve seal pressure a. Decrease LC system pressure.
rapidly. against valve
b. Particulate matter in valve b. Use an inline filter before the injection
valve.
c. Inadequately filtered sample c. Filter with a 0.5 μm filter before
injection.
d. Buffer crystallization d. Do not allow buffers to stand in
system. Run a flush sequence from the
Commands menu when the system is
not in use.
19. Injection from a. Incorrect vial position entered in a. Check Samples menu.
incorrect vial. Samples menu
b. Sample placed in incorrect b. Check tray arrangement.
position in vial tray
20. Samples are injected a. Error in file (calibration vials a. Check file (calibration template).
incorrectly in a pattern. placement)
Needle
21. Needle is bent or a. Incorrect vials a. See list of recommended replacement
broken. parts in the front of the manual.
b. Alignment problem b. Call Thermo Fisher Scientific.
c. Arm sticking c. Call your Thermo Fisher Scientific
22. Needle is plugging. a. Multiple/incorrect septa a. Verify a single septum of the type
recommended.
Syringe
23. Syringe drive creates a. Defective limit switch a. Call your Thermo Fisher Scientific
loud buzzing. service representative.
24. Flush valve will not a. Defective valve/coupler/motor a. Call your Thermo Fisher Scientific
activate. service representative.
25. Flush valve is actuated, a. Plugged inlet filter in solvent a. Replace inlet filter (see “Replacing the
but syringe cannot reservoir Flush Solvent Inlet Filter” on
draw flush solvent. page 115).
Arm
26. Hook does not lift vial. a. XYZ arm motor stepping failure a. Call your Thermo Fisher Scientific

7 Troubleshooting
Display Messages

Leaks
27. Leakage during loop a. Blocked loop or valve not a. Flush sample loop or replace; check
filling deflected far enough and flush waste line. Check the sensor.
28. Cross-port leakage a. Worn rotor seal a. Replace according to instructions in
“Replacing the Rotor Seal” on
page 109.
29. Liquid on vial caps a. Leaky flush valve a. Replace flush valve.
b. Leaky injection valve b. Replace rotor seal (see “Installing the
Rotor Seal” on page 112).
Other
30. An automatic sequence a. Column-oven, heater, door a. Check the Ready Participation menu.
is interrupted, or interlock activated
instrument will not
start.
31. In Stand Alone mode, a. Configuration incorrectly set to a. In the Configurations menu, set Mode
Status Screen indicates SpectraNet mode to Stand Alone.
a run in progress, but
the instrument is
locked up.
32. Sample is a. Dirty vials a. Replace vials.
contaminated. b. Improper septa made of silicone or b. Use recommended septa. Thermo
other rubber-like material Fisher Scientific septa are made of
Teflon-faced silicone.
33. System pressures are a. Block between column and a. Crack each fitting and observe
elevated. autosampler pressure. See instructions in “Testing
for Tubing Restrictions” on page 144.
Display Messages
As mentioned in Chapter 2, “Installation,” three different kinds of messages can appear on
your autosampler display: user messages, confirmation messages, and error messages. This
section describes the possible conditions that generate these messages.
• User Messages
• Confirmation Messages
• Error Messages

7 Troubleshooting
Display Messages
User Messages
User messages are displayed as a result of the user’s incorrect action.
User message Description

Autosampler Busy You cannot issue a command from a menu or
press a key while the autosampler is in the middle
of a previously requested operation.
Autosampler Busy No Loading Allowed You cannot load a sample set while the queue is
running.
Cannot Add Priority Set During Final You cannot add a priority set during bracketing
Calibration (after all the sample vials have been injected).
Cannot Add Priority Set at This Time You cannot add a priority set to other than set 1.
You cannot add a priority set unless the file's
Calibration menu calls for interspersed
calibration vials (you must select Reuse
calibration vials if you want to add priority sets
to the queue).
File in Queue Cannot Be Copied To You cannot copy to a file assigned to a sample set
in the queue.
File In Queue Cannot Be Deleted You cannot delete a file assigned to a sample set
in the queue.
File In Queue Cannot Be Edited You cannot edit a file assigned to a sample set in
the queue from the Edit menu. You can edit the
run-file copy of the active file from the Samples
menu.
File Protected Cannot Be Copied To You cannot copy to a file that is protected
(Protect is set to On) in the Configurations
menu.
Use Samples Key to Add Samples to You cannot start a run by pressing the RUN key
Queue when the queue is empty. You must first load or
add sample sets to the queue.

7 Troubleshooting
Display Messages
Confirmation Messages
Confirmation messages inform you that the autosampler is completing a requested operation
or command. These messages disappear when the operation is complete.
Confirmation message Description

Aligning Arm The Align Arm command is in progress.
Clearing Mixer The Clear Mixer command is in progress.
File Copied The requested file has been copied.
File Deleted The requested file has been deleted.
File Loaded The requested file has been loaded into the queue.
Flush Sample Syringe The Flush Sample Syringe command is in progress.
Homing Arm The Home Arm command is in progress.
Initializing The Initialize Hardware command is in progress
(see“Initialize Hardware” on page 97).
Set Added to Queue The requested sample set has been added to the sample
queue.
Error Messages
There are three kinds of errors: hardware errors, system errors, and diagnostic errors.
This topic describes these types of errors:

• “Hardware Errors” on page 140
• “System Errors” on page 143
For descriptions of diagnostic errors, see “Diagnostics in the Tests Menu” on page 101.
Hardware Errors
Hardware errors occur during the normal use and operation of the instrument. Most of the
time you can clear these errors. For some, you might need to call your Thermo Fisher
To clear the error message, press any key, and then take the steps suggested for each message in
Table 26 to resolve the problem.

7 Troubleshooting
Display Messages
Table 26. Hardware error messages (Sheet 1 of 3)

Hardware error message Description
Arm Failed to Home on X, Y, Z The XYZ arm could not make the final x-, y-, or
z-axis motion required to return to the home
position. Check for a dislodged vial, tray, or other
obstruction. Run the Initialize Hardware routine. If
the error persists, contact your Thermo Fisher
Arm Jam on X, (Y, Z) Axis The XYZ arm is obstructed on its left-to-right (x)
axis, its front-to-back (y) axis, or its vertical (z) axis.
Check for a dislodged vial, tray, or other obstruction.
Run the Initialize Hardware routine. If the error
persists, contact your Thermo Fisher Scientific
Flush Valve Misaligned The flush valve did not turn all the way to the
required position. Perform the Initialize Hardware
routine. If the error persists, run the Test Connectors
routine. If the error persists, contact your Thermo
Fisher Scientific service representative.
Hardware Failure A problem occurred with the valves or syringes. Run
the Initialize Hardware diagnostic (see “Initialize
Hardware” on page 97), the Injector Test (see
“Injector” on page 97), or both. If you are unable to
clear the error, contact your Thermo Fisher Scientific
Hardware Not Homed The solvent valve could not move to a certain
requested position, but the hardware was not
initialized properly. Or, on power-up, the solvent
valve could not home properly. Run the Initialize
Hardware diagnostic (see “Initialize Hardware” on
page 97). If you are unable to clear the error, contact
your Thermo Fisher Scientific service representative.
Hardware Timeout Time ran out for completing the requested
mechanical operation. The problem could be with
the arm, valves, or syringes. Run the Initialize
Hardware routine (see “Initialize Hardware” on
page 97). If the problem persists, try manually
flushing the syringes using the Flush Sample and
Flush Prep Syringe commands (see “Flush Sample
Syringe” on page 96). If the problem persists, contact

7 Troubleshooting
Display Messages

Injector Valve Failure The injection valve failed to move (between the
INJECT and FILL positions, or vice versa) for the
requested operation. Issue the Injector command
from the Commands menu. If the error persists, call
Inject Valve Misaligned The injection valve is positioned between the
INJECT and FILL positions. Run the Injector test
(see “Injector” on page 97), and call your Thermo
Fisher Scientific service representative if the error
persists.
IValve Move Is Impossible The injection valve cannot move to the requested
position from its current position. Switch the
injection valve position using the Injector command,
and call your Thermo Fisher Scientific service
representative if the error persists.
IValve Move Not Detected The system did not detect a requested movement to
the required position. Check for a loose connection
to the injection valve. Try manually moving the
injection valve to another position. If the error
persists, call your Thermo Fisher Scientific service
representative.
Inject Valve Overshoot The injection valve moved past the desired position.
Run the Injector test (see “Injector” on page 97), and
call your Thermo Fisher Scientific service
representative if the error persists.
Injector Valve Undershoot The injection valve failed to move far enough to the
desired position. Run the Injector test (see “Injector”
on page 97), and call your Thermo Fisher Scientific
service representative if the error persists.
Parameter Out of Range You entered a value that was too large or too small.
For example, you entered an injection volume that
was too large for the installed syringe. Check the
installed syringe/sample loop versus the edit file
parameters.
Syr 1(2) Not Enough to Expel The syringe is not retracted far enough to expel the
requested volume flush operation. Run the Initialize
Hardware test (see “Initialize Hardware” on page 97),
and restart the flush cycle.

7 Troubleshooting
Display Messages

Syringe Failure The syringe failed to move to the appropriate
position required for an operation. Run the Initialize
Hardware test (see “Initialize Hardware” on page 97).
If the error repeats, call your Thermo Fisher Scientific
Syringe Overfill You requested an injection volume that is too large
for the size of the installed syringe. Check the
method and syringe volume.
Unexpected Vial in Hook A vial was found in the hook where no vial was
expected for the requested operation. To clear the
error, remove the vial and restart or resume the
requested operation.
Vial Not Found in Hook No vial was found in the hook where one was
expected. Verify that a vial exists in the requested tray
location, check the file and vial assignments in the
Samples menu, and check to see if a vial is lodged in
the sample tower. (If so, the needle might be bent.)
System Errors
System errors occur very rarely but they cancel normal operation. Because system errors are
not usually problems you can correct, they are listed in this section but not described. If you
see these or other messages, document them and contact your Thermo Fisher Scientific
service representative for assistance.
Invalid Current Location
Invalid Command
Not in GET/RET Sequence
Z Must be Up/No Vial
Move Z Not Allowed
Get LocNum: Bad Row, Col
Z up Only in Serv Block
Invalid Target Location
SValve Extra Interrupt
Bad Vial Number
Unexpected Syr Event

7 Troubleshooting
Testing for Tubing Restrictions
Testing for Tubing Restrictions

If the solvent lines are restricted, you will probably hear a loud grinding sound from the
syringe-drive mechanism due to increased resistance to syringe travel.
IMPORTANT Before beginning this procedure, be sure to set up a beaker or other

container to catch the solvent.
Y To isolate a block to a section of tubing
1. Place the autosampler injection valve into the FILL position (press the MENU key and
select COMMANDS > Injector > Rotate Injection Valve, and press the [+] and [–] keys
to select Fill).
2. Disconnect the tubing from port 3 of the injection valve.
3. Initiate a flush sequence (press the MENU key and select COMMANDS > Flush
Sample Syringe (see “Flush Sample Syringe” on page 96). Solvent flows freely on the
return stroke of the plunger if there are no restrictions present. Flow restriction is unlikely
at this point due to the large internal tubing diameter.
4. Reconnect the tubing.
5. Disconnect the needle and check the flow.
6. If no restriction is found, reattach all of the tubing, and flush the syringe to verify that the
restriction still exists.
7. If a restriction is still present, remove and clean the sample needle as described in
“Maintaining the Sample Needle Module” on page 115.

8
Replaceable Parts
When you must replace parts for use with your SpectraSYSTEM autosampler, refer to this list
of spare parts, consumables, and kits available from Thermo Fisher Scientific.
Contents
• Clear Vials and Vial Kits
• Amber Vials and Vial Kits
• Cables and Adapters
• Standard Autosamplers
• Inert/Biocompatible Autosamplers
• Test Mixes
• Upgrade Kits
Clear Vials and Vial Kits

Shell Vials
Shell vials, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4946-010
Shell Vial Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4948-010
Standard Vials
Standard vials, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4951-010
Standard vial septa, 100/package. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4952-010
Standard vial caps, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4953-010
Standard Vial Kit, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4954-010
Crimp Vials/Caps
Crimp caps, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4955-010
Crimp vials, 100/package, 1.8 mL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4956-010
Crimp Vial Kit, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4957-010
Poly Kits
Polypropylene Kits, 600 mL, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . A4958-010
Polypropylene Kits, 100 mL, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . A4959-010
Inserts
Spring for insert, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4981-010
Insert, 50 mL, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4960-010
Insert, 100 mL, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4961-010

8 Replaceable Parts
Amber Vials and Vial Kits

Crimp Vials
Amber crimp vials, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4964-010
Amber Vial Crimp Kit, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4965-010
Standard Vials
Standard amber vials, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4966-010
Standard Amber Vial Kit, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4967-010
PFTE Liners/Septa
PTFE Liners, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4968-010
PTFE Vial caps/septa, 100/package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4969-010
Standard vial station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4970-010
Sample Trays
Three sample trays, 35-vial capacity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3696-010
Cables and Adapters

Autosampler-to-integrator cable/adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3981-010
BCD Communications option
(This option requires field installation by
Thermo Fisher Scientific unless purchased
simultaneously with a SpectraSYSTEM autosampler.) . . . . . . . . . . . . . . . . . A3663-010
Standard Autosamplers
Injector valve assembly for the AS3000, 100 mL, stainless steel
(Assembly includes the complete autosampler valve assembly.) . . . . . . . . . . . A3566-030
Standard Maintenance Kit (Kit includes everything necessary to
maintain the instrument for one year: inlet filter,
needle replacement kit, valve rotor seal, syringe,
lubricant, cleaner, and LC test sample.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4101-010
Standard Fittings Kit (Kit includes stainless steel fittings and tubing
used in a SpectraSYSTEM LC system.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4051-010
Autosampler Needle Replacement Kit
(Kit includes the standard, stainless-steel,
deflected-point replacement needle.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4719-010
Standard Sample Loops and Syringes
Rheodyne sample loop, 20 μL, stainless steel . . . . . . . . . . . . . . . . . . . . . . . . 3302-0230
Rheodyne sample loop, 50 μL, stainless steel . . . . . . . . . . . . . . . . . . . . . . . . 3302-0010
Rheodyne sample loop, 100 μL, stainless steel . . . . . . . . . . . . . . . . . . . . . . . 3302-0020
Rheodyne sample loop, 1 mL, stainless steel . . . . . . . . . . . . . . . . . . . . . . . . . 3302-0040
Screw-tip syringe, 250 μL, (standard) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3588-020
Screw-tip syringe, 500 μL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3588-010
Solvent inlet filter cartridge (pkg. of four). . . . . . . . . . . . . . . . . . . . . . . . . . . A4094-010

8 Replaceable Parts
Inert/Biocompatible Autosamplers
Injector Valve Assembly
(The assembly includes the complete autosampler valve assembly.) . . . . . . . . A3566-020
Inert/Biocompatible Maintenance Kit
(The kit includes the inert/biocompatible versions of everything in
the Standard Maintenance Kit.) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4102-010
Inert/Biocompatible Fittings Kit
(The kit includes PEEK fittings and tubing used in an
inert/biocompatible SpectraSYSTEM LC system.) . . . . . . . . . . . . . . . . . . . . A4061-010
Autosampler Needle Replacement Kit (Kit includes the standard,
inert, deflected-point replacement needle.) . . . . . . . . . . . . . . . . . . . . . . . . . . A4719-020
Inert/Biocompatible Sample Loops and Syringes
Rheodyne Sample Loop, 20 μL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4169-010
Rheodyne Sample Loop, 50 μL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4169-020
Rheodyne Sample Loop, 100 μL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4169-030
Rheodyne Sample Loop, 1 mL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4169-060
Rheodyne Sample Loop, 2 mL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4169-070
Screw-tip Syringe, 250 μL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3588-020
Screw-tip Syringe, 500 μL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A3588-010
Solvent Inlet Filter Cartridge (pkg. of four) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4094-010
Test Mixes
Autosampler Test Mix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A4991-010
Autosampler Dilution Test Mix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A5135-010
Upgrade Kits
Upgrade kits are available for SpectraSYSTEM stainless steel autosamplers. Contact your local
Thermo Fisher Scientific representative for details.

A
Quick Reference Guides

Use the following two-page guides to familiarize yourself with the SpectraSYSTEM AS3000
autosampler’s command center.
Tip To control the autosampler from the command center, set the Options >
Configurations > Mode field to Stand Alone.
Contents
• SpectraSYSTEM AS3000 Menus
• SpectraSYSTEM AS3000 Quick Reference Guide
• Quick Start: Starting Runs from the Command Center

SpectraSYSTEM AS3000 Menus
page 1 of 2
MENU SAMPLES STATUS RUN

FILES QUEUE TESTS Sample Set 1 QStatus Set #Samples Starts a run.
COMMANDS OPTIONS File 1: IDLE 0/ 0
Injection Volume* 10 Status Vial Vol #Inj
Injections/Sample 1 NOTRDY 10 0/ 0
Cycle Time 10.0 File 1:
First Sample Vial A01 Oven Tray Temp If the queue is empty,
Number of Samples1 OFF 18 OFF 0 the following message appears.
Add to Queue? Yes
**Use SAMPLES Key**
*Becomes Loop Size if Injection Type = Full to Add Samples to the Queue
Injection
If the queue contains
Injection Volume* 10 one or more sample sets,
Injections/Sample 1 the QStatus changes from
Edit Cycle Time 10.0 IDLE to RUN.
FILES Col Oven Off Temp 18
Edit File 1 Tray Temp Off Temp 0
QStatus Set #Samples
Edit Load File Name *Becomes Loop Size if Injection Type = Full RUN 1 1/ 1
Copy Delete Injection
Calibration Calibration
Timed Events STOP
More Number of Levels 1
QUEUE Samples/Calibration 0 Pauses a run.
Load Injections/Level 1
Order File Name Set Injection Volume 10 When you press STOP,
1 1 Type Reuse same vials the following message appears.
Load File 1: Bracket Samples No
STOP requested
TESTS (see page 2) Copy Timed Events Select Abort Sample
Continue
Copy File 1: Time TF1 TF2 TF3 TF4
COMMANDS (see page 2) To File 1: 0.00 Hi Hi Hi Hi
oTo stop the run
Delete 1. Select Abort Sample.
More
OPTIONS (see page 2) 2. Press Stop a second time.
Delete File 1: Equilibration Time 0.0

Gradient Delay 0.00
Sample Viscosity Normal oTo continue the run
Flush Volume 400 Select Continue.
Injection Type Push Hi
Injection Range 1-200
Needle Height 2.0

SpectraSYSTEM AS3000 Menus
page 2 of 2
Software Version RAM Test Test Comm Port
Install Loopback Cable

Version x.yy.zz RAM: PASS
CONTINUE
TESTS
Display Input States ROM Test Initialize EEPROM
Software Version
Display Input States Pump Ready Inj Hold Reset all system values
ROM: PASS
Display Output States Lo Lo Are you sure? No
Display Output States Hardware Test
RAM Test
ROM Test AS Rdy Inject Grad Stop
Hardware Test Connector: PASS
Hi Hi Hi Hi
Test Comm Port Display Timed Events Test External Contacts
Initialize EEPROM
TF1 TF2 TF3 TF4 Disconnect all external
Hi Hi Hi Hi contacts CONTINUE Total System Cycles
Total Cycles Note

0 01 May10
OPTIONS Configurations Input Polarity Maintenance Log
Configurations Sample Syringe 250 Pump Ready Active Hi Total System Cycles
Ready Participation Prep Installed No Inj Hold Active Hi Injector Valve
Input Polarity Oven Installed Yes Needle Wear
Output Polarity Tray Temp Installed Yes Output Polarity Sample Syringe Maintenance Log Menus
Shutdown Key Repeat Rate Medium
Maintenance Log File Name Protect Autosampler Ready Lo #Cycle Due Note
Communications 1: Off Inject Out Active Lo 0 12000 01May10
2: Off Grad Start Active Lo Reset #Cycles No
3: Off Pump Stop Active Lo
4: Off Shutdown
Mode Stand Alone
Delay Time Off Communications (Stand Alone mode only)
Oven Shutoff Yes
Tray Temp Shutoff No Baud Rate 9600
Ready Participation Pump Shutoff Yes Parity NONE
Flush Volume 400 Flow Control NONE
Door Interlock ENABLE
Data Bits 8
Tray Temp Ready ENABLE
Stop Bits 1
Col Oven Ready ENABLE
Echo On
COMMANDS
Flush Sample Syringe Initialize Hardware Injector Arm
Initialize Hardware Flush 500 µL “Initializing” Rotate Injection Valve Home Arm
Injector Inject Align Arm A01
Arm

SpectraSYSTEM AS3000 Quick Reference Guide
Y To accept values
Press the ENTER, MENU, or STATUS keys or use the
FILES QUEUE TESTS
arrow keys.
COMMANDS OPTIONS
Installing Trays
Trays A, B, and C are arranged from left to right in the sample tub.
RUN STATUS MENU The position number is indicated on the top left of each vial position.
STOP
Y To install your trays
ENTER 1. Hold the tray handle and tilt the back end down.
2. Insert the tray's runner into the slots at the back of the sample tub
Samples SpectraSYSTEM AS3000 and lower the front of the tray into place.
3. Press down firmly to seat the tray and pull the handle back
toward you to be sure the tray is properly seated.
Using the Keypad
Managing Files
RUN Starts a run. Y To set up a file
STOP Pauses the sample queue. You can continue the run 1. Press MENU and select FILES > Edit.
from the current vial or cancel the run and return 2. Enter the file number and name.
to the beginning of the sample queue.
3. Select Injection.
Samples Opens a menu where you can specify the injection
4. Enter the injection volume, number of injections per vial, and
parameters and a file name for a sample set, add
cycle time, and set the oven and sample tray temperatures.
sample sets to the queue, and edit runs in progress.
5. Select Calibration.
STATUS Displays the status screen.
6. Enter the number of standard levels, calibration interval, number
, , , Moves the cursor in the direction indicated on the of injections per level, and injection volume. Select the type of
and key. The UP and DOWN arrow keys also move calibration routine (reuse or intersperse calibration vials). Select
the cursor between menus and displays. whether or not (yes or no) you want the sample set to end with a
MENU Displays the main menu. For information on the calibration set.
menus, refer to the AS3000 Menus sheet. 7. To program external events, select Timed Events and program a
and Scrolls you through a field's available choices or time and state (Hi or Lo) for up to four time functions.
changes the value of alphanumeric entries. 8. Select More.
ENTER Accepts a selection or menu entry; also advances 9. Select the injection type: Full, Pull, Push Hi, or Push Lo. Enter
the cursor to a new field. the equilibration time, gradient delay, flush volume, and needle
height values for your application.
Setting Parameters Y To load a file
Y To enter values 1. Press MENU and select FILES > Load.
• For numeric entries, use the or key to increase or 2. Select the file number and press ENTER .
decrease the value of each digit.
Y To build the sample queue
• For alphanumeric entries, use the and keys to scroll
1. Press the Samples key.
through the alphabet from A to Z, then through numbers 0 to 9,
and then slash, hyphen, and blank space. 2. Enter the file number in the Use File field.
• For preset choices, use the key to advance through a preset 3. Press ENTER to accept the other values in the Samples Menu
list of choices. The key takes you back through the list. and to add the file to the Queue (Yes).
© 2010 Thermo Fisher Scientific Inc.

All rights reserved.
Y To run a file Y To add a set to the queue
1. Press RUN to start the run. 1. Press the Samples key.
2. To monitor the sample queue, vial injection, and column and tray 2. Enter the file number and set to add to the queue.
temperatures, press STATUS . 3. Accept the Edit file parameters and press ENTER in the Add to
3. To pause a run, press STOP . Queue? field.
STOP requested appears. Y To delete a set from the queue
4. Do one of the following: 1. Press MENU and select QUEUE.
• To cancel the run, select ABORT Sample, and then press 2. Move the cursor to the line to be deleted.
STOP again.
3. Decrement the Order value to 0 and then blank. Moving the
• To continue the run, select Continue. cursor deletes the blank line from the display.
Y To edit a run in progress Y To add a priority set
You can edit some of the file parameters for the run in progress from A priority sample set is inserted into the active (currently running)
the Samples menu. run before other samples in the set. It uses the same file name as the
1. Press the Samples key. Press . active set.
2. Edit the Injection Volume, Injections/Sample, Cycle Time, and
Number of Samples values. Note When running priority sets, remember the following:
You can edit the Calib 1 (of X) value only if you have selected • If you are running calibration vials in the priority set, you
Reuse vials as your calibration routine. You cannot edit the First must select Reuse vials as your calibration routine.
Sample Vial value. • You cannot change the order of a priority set in the queue.
Except for the Cycle Time and Calib 1 (of X) values, changes take 1. Press the Samples key.
place on the next sample injection. A cycle time change affects the 2. Use the key to change the Set field value to P.
current sample injection, a Calib 1 (of X) change affects the next
3. Fill in the other file parameters as for any other set.
recalibration.
4. Add the priority set to the queue.
Y To delete a file 5. Press MENU and select QUEUE. The priority set has an Order
1. Press MENU and select FILES > Delete. value of 1, has the same File Name as the active file, and is
2. Select the file number to be deleted. indicated by a P in the Set field.
3. Press ENTER .
Changing Your Autosampler's Setup
Y To copy a file
Y To change the cursor speed
1. Press MENU and select FILES > Copy.
2. Select the file number to be copied from the Copy file field, and You can adjust the cursor speed and display contrast.
the file number to be copied to the To file field. 1. Press MENU and select OPTIONS > Configurations.
3. Press ENTER . 2. Move the cursor to the Key Repeat Rate field.
3. Use the and keys to select between Slow, Medium, and
Y To protect a file
Fast.
1. Press MENU and select OPTIONS > More.
2. Scroll down to the File Name and Protect fields. Select On in the Y To change the display contrast
appropriate file's Protect field. 1. Press STATUS to access the Status Screen.
3. Press ENTER . 2. Press .
Managing the Queue • To increase the contrast, use the key.
Y To reorder sets in the Queue • To decrease the contrast, use the key.
1. Press MENU and select QUEUE.
Y To turn off the door interlock
2. Move the cursor to the line where you want the change to occur
and increment or decrement to the new Order value. When the door interlock is enabled, the XYZ arm moves to the
3. Move the cursor out of the field to automatically rearrange the back-left corner of the tray compartment when you open the door.
lines. Y To turn off the interlock
1. Press MENU and select OPTIONS > Ready Participation.
2. Move the cursor to the Door Interlock field and use the and
keys to select DISABLE.
154
Quick Start: Starting Runs from the Command Center
This guide describes how to start runs from the command center. If
you have not set up your LC system, inject distilled water rather than Setting the Operation Mode to Stand Alone
an actual sample.
Y To set the operation mode to Stand Alone
Contents 1. Turn on your autosampler by pressing the on/off switch in the
lower right corner of the autosampler.
• Command Center
When the startup sequence is complete, the Status screen appears.
• Loading Trays into the Autosampler
Figure 2. Status screen
• Setting the Operation Mode to Stand Alone
• Starting a Run QStatus Set #Samples
IDLE 0 0/ 0
2. Press MENU and select Options > Configurations.
Command Center
3. Press to move down the Configurations menu.
For information on the menu screens, see “SpectraSYSTEM AS3000 4. In the Mode field, select Stand Alone.
Menus.” For information on the keypad controls, see the
“SpectraSYSTEM AS3000 Quick Reference Guide.” Starting a Run
Figure 1. Command center
To start a run, do one of the following:
• To customize the injection settings, follow these steps:
− Step 1: Creating Your File
FILES QUEUE TESTS
COMMANDS OPTIONS − Step 2: Loading Your File
− Step 3: Building a Sample Queue
− Step 4: Starting Your Run
RUN STATUS MENU • If you want to use the default settings, go directly to these steps:
STOP − Step 3: Building a Sample Queue
− Step 4: Starting Your Run
ENTER
Step 1: Creating Your File
Samples SpectraSYSTEM AS3000
Create files when you want to use more than one set of injection
parameters in the queue, when you want to store a specific set of
injection parameters, or both.
Loading Trays into the Autosampler The default file contains these parameter settings.
Trays A, B, and C are arranged from left to right in the sample tub. Menu parameters Default setting
The position number is indicated on the top left of each vial position.
Injection
Y To install your trays Injection Volume 10 μL
1. Fill a vial with distilled water. Injections/Sample 1
2. Place the vial in position 1 of tray A, location A01.
Cycle Time 10.0 minutes
3. Hold the tray handle and tilt the back end down.
Column Oven Off
4. Insert the tray's runner into the slots at the back of the sample tub
and lower the front of the tray into place. Tray Temp Off
5. Press down firmly to seat the tray and pull the handle back
toward you to be sure the tray is properly seated.
© 2010 Thermo Fisher Scientific Inc.

All rights reserved.
Menu parameters Default setting Step 2: Loading Your File
Calibration Y To manually load your file
The default value in the Samples/Calibration field is zero, which 1. Select Edit > Load.
means that the sample set contains no calibration vials and the
2. Verify that File 1 is entered, and then press ENTER to load it
autosampler ignores the other settings in the Calibration menu.
into the autosampler's active memory.
Number of Levels 1
The **File Loaded** message appears briefly, and then the Status
Samples/Calibration 0 screen appears (Figure 4). Loading the file activates the
Injections/Level 1 temperature control options that you set in the Injection menu.
Figure 4. Queue Status screen
Injection Volume 10
Type Reuse same vials QStatus Set #Samples
IDLE 0 0/ 0
Bracket Samples No
More Step 3: Building a Sample Queue
Equilibration Time 0.00 minutes Y To build a sample queue
Gradient Delay 0.00 mL 1. Press the Samples key to display the Samples menu.
Sample Viscosity Normal If you have not loaded a file, the File field is blank.
Flush Volume 400 μL Figure 5. Samples menu
Injection Type Push Hi Sample Set 1
File 1:
Injection Range 1–200 μL
Injection Volume 10.0
Needle Height 2 mm Injections/Sample 1
Cycle Time 10.0
Y To create your file First Sample Vial A01
1. Press MENU and select FILES > Edit. Number of Samples 1
Add to Queue YES
The Edit menu appears.
Figure 3. Edit menu 2. To move down the Samples menu, press .
Edit File 1_ 3. To change the Cycle Time to 1.0, use the , , ,
File Name: PRACTICE and keys.
The cycle time is the time between injections. If you are injecting
Injection
Calibration an actual sample, enter an appropriate cycle time for your
application (injection time + data acquisition time).
Timed Events
4. When you reach the Add to Queue line, press ENTER to add the
More
sample set (1) to the queue.
2. Press ENTER to edit File 1.
3. Use the use the , , , and keys to specify Step 4: Starting Your Run
each character in the file name of your choice. For this example,
Y To start your run
enter the name PRACTICE.
1. If you have not already done so, place a vial filled with distilled
4. Move the cursor to each field in the Injection, Calibration, Timed
water in position A01.
Events, and More menus and press ENTER to accept the default
values. 2. Press RUN .
If everything is running properly, the QStatus changes from
Note After the last field in each menu, the next most IDLE to RUN (Figure 6). The autosampler picks up the vial,
probable choice in the menu structure appears. For example, carries it to the sample tower, injects the sample, returns the vial
after you accept the default values in the Calibration menu, to the sample tray, and flushes the lines.
the screen returns to the Edit menu with the cursor in the
Figure 6. Queue Status screen with the queue running
Timed Events field. Similarly, after you accept the default
values in the More menu, the screen returns to the File menu QStatus Set #Samples
with the cursor in the Load field. This pattern occurs RUN 1 1/ 1
throughout the user interface. You can override the default The injection status field displays the time elapsed since the run
choice at any time by moving the cursor where you like. started (Figure 7). When the run ends, the QStatus returns to
IDLE.
Figure 7. Injection Status screen with a run in progress
Status Vial Vol #Inj

0.05 A01-S 10 1/ 1
156
I
Index
Symbols cables
communication 31
#Inj 85
contact closure 37
#Samples 83
carryover, sample 52–55
caution, defined xiii–xiv
A checklist, startup 14
A/S Ready pin, back panel 42 column compartment cover, installing 27
Abort/Continue menu 89 column oven
Align Arm command 98 description 3
arm temperature control 68
misaligned 136 column, installing 25
movement restricted 136 Commands menu 96
Arm menu 97 communication among the system modules 30
arrow keys 60 Communications menu 43
AS3000 photograph 1 compliance
autosampler ready signal 45 regulatory iii
WEEE v
Configurations menu 91
B
confirmation messages 62
back panel pin connections 42
contact closure cable assembly 37
backlash 97
conventions used in manual
baud rate, Communications menu 44 Cautions xiii–xiv
BCD interface 46 Tips xiv
bench space requirement 16 cursor
bent needle 135 square and blinking 58
biocompatible, replaceable parts 147 triangular 58
blinking square cursor 58 cycle time, Injection menu 68
blocked
injector valve 136
needle 136
D
sample loop 136 data bits, Communications menu 44
bracket samples, Calibration menu 71 data system control 30
broken vials, cause of 136 delay time for shutdown 123
building ground, connecting the autosampler to xiv, 19 detector, connecting the plumbing 26
diagnostics 101
Display Input States menu 103
C Display Output States menu 103
cable connections Display Timed Events menu 104
contact closure 38
DOOR status 84
SN4000 controller 33
drop catch, flushing 118

Index: E
E Injection menu 66
injection range 76
echo, Communications menu 44
injection types
Edit menu 64
description 4
EEPROM, initializing 106
selections 75
electrical requirements 17
injection volume
EPROM firmware, SN4000 controller 33 range 67
equil status 83 recommended 93
equilibration time, More menu 74 injections per level, Calibration menu 70
error messages 62, 140 injections per sample, Injection menu 67
external contacts, testing 105 Injector command 97
injector valve
F disassembling 111
File # 85 testing 97
files Injector Valve menu 125
loading 77 input pins, back panel 40
managing 90 input signal polarity 44
flow control, Communications menu 44 integrators, using 46
flush solvent bottle, connecting 21 intersperse vials, Calibration menu 71
flush solvent inlet filter, replacing 115
Flush Syringe menu 96 K
flush volume, acceptable range 74 keypad keys 59
full-loop injection type 4 kits, BCD Communication 47
fuses, replacing 122
L
G lift points, autosampler 17
GRAD status 84
gradient delay
determination 99 M
More menu parameter 74 main menu 61
Gradient start pin 41 maintenance log 124
gradient start signal 45 maintenance procedures
Ground pin, back panel 41 changing the sample loop 121
grounding post xiv, 19 cleaning the sample needle module 115
emptying the flush-solvent tray 109
flushing the drop catch 118
H flushing the solvent inlet filter 115
hardware error messages 140 replacing the fuses 122
Hardware test 105 replacing the rotor seal 109
hardwire connections 43 replacing the syringe 118
high voltage, defined xiii manual set, SpectraSYSTEM user guides 19
hot surface, defined xiii MENU key 60
menu trees 151
menus
I Abort/Continue 89
inert, replaceable parts 147 Arm 97
Initialize Hardware command 97 Calibration 69
inj hold signal 45 Commands 96
Inject Hold pin, back panel 41 Communications 43
Inject Out pin, back panel 41 Configuration 91
inject out signal 45 Copy 90

Index: N
menus (continued) polarity setting 44

Delete 90 priming the autosampler 29
Edit 64 protective earth ground, connecting the autosampler to xiv
Flush Syringe 96 pull-loop injection type 5
Injection 66 Pump Ready pin, back panel 41
Injector Valve 125
pump ready signal 45
Input Polarity 44
pump shutoff 124
Load 77
Pump Stop pin, back panel 41
Maintenance Log 125
More 74 pump stop signal 45
Needle Wear 127 PushLoop injection type 6
Output Polarity 45
Ready Participation 48 Q
Sample 78
Queue menu 80
Sample Syringe 127
quick reference guides
Shutdown 123
SpectraSYSTEM AS3000 Menus 151
Tests 101
Timed Events 72 SpectraSYSTEM AS3000 Quick Reference Guide 153
Total System Cycles 125 Starting Runs from the Command Center 155
messages
Arm,* 105 R
Opt Config 105 RAM test 104
types 62 Ready Participation menu 48
module Identification, test result 102 regulatory compliance iii
More menu 74 replaceable parts 145–147
reproducibility, injection volume 50
N reuse same vials, Calibration menu 71
needle height RJ45 to DB9 adapter 34
More menu field 76 ROM test 104
optimizing 95 rotor seal, replacing 109–113
needle module, cleaning 117 RS-232 communication ports, data system computer 34
needle plugging 137 RUN key 59
Needle Wear menu 127 runs
number of levels, calibration 70 starting from the command center 81, 156
stopping from the command center 88
O
ordering information, replaceable parts 145 S
output pins, back panel 40 safety and special notices, defined xiii
output signal polarity 45 safety icons xiii–xiv
oven shutoff 124 safety standards iii
sample loop, changing 121
sample needle module, replacing or cleaning 115
P
sample sets, priority 87
parity, Communications menu 44
sample trays, installing 27
pause status 83 Samples key 60
pin assignments, back panel 40
Samples menu
pin connections 42 adding samples to the queue 78
plumbing connections troubleshooting 137
connecting the autosampler to the detector 26 samples per calibration, Calibration menu 70
installation procedures 21
schedule, maintenance 108
plus and minus keys 60
set temperature, checking 85

Index: T
shipping kit 19 troubleshooting

Shutdown menu 123 autosampler hardware problems 135
signal polarities, SpectraNET mode 36 autosampler specific chromatography problems 132
SN4000 controller general chromatography problems 129
back panel 31 TTL input and output signals 103
bottom 32 tubing restrictions, testing for 144
U12 socket and communication ports 33
SN4000 controller, connecting the cables to 32 U
software version 103
uninterruptible power supply (UPS) 17
solvent waste container, installing 22
user guides, SpectraSYSTEM 19
specifications, autosampler 11
SpectraNet mode 30
Stand Alone mode 30 V
startup, autosampler 29 variable-loop injection 67
stator, cleaning 112 Vial Not Found in Hook error message 143
STATUS key 59 vials
Status Screen 61 appropriate caps for 27
stop bits, Communications menu 44 position numbering 27
STOP key 59 total number is sample set 72
type S or C 84
syringe
flushing 96 viscosity
injection volume range 94 changing the draw rate based on 94
replacing 118–120 normal, medium, or viscous 74
syringe speed, appropriate for solvent viscosity 94
system errors 143 W
system synchronization harness 37 waste solvent container, installing 22
WEEE compliance v
T weight, autosampler 16
temperature control
column oven 68
tray compartment 68
tests
COMM port 106
diagnostic 101
External Contacts 105
flush sample syringe 96
Hardware 105
Initialize EEPROM 106
performance verification 49
RAM 104
ROM 104
tubing restrictions 144
Tests menu 101
Timed Events menu 72
Tips, defined xiv
Total System Cycles menu 125
tray compartment, temperature control 68
trays, installing 27
triangular cursor 58

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Release history: Revision A, released June 2010

For Research Use Only. Not for use in diagnostic procedures.

EN 55011: 2007; A2:2007 EN 61000-4-4: 2004

Low Voltage Safety Compliance

Notice on Lifting and Handling of

Notice on the Proper Use of

Notice on the Susceptibility

For manufacturing location, see the label on the instrument.

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

Electric Shock: This instrument uses

Chemical: This instrument might contain

Heat: Before servicing the instrument,

Fire: Use care when operating the system

Eye Hazard: Eye damage could occur

General Hazard: A hazard is present that

When the safety of a procedure is

Chapter 2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide ix

Communication: SpectraNet or Stand Alone . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Chapter 3 Keypad Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .57

Chapter 4 Standalone Operation from the Command Center. . . . . . . . . . . . . . . . . . . . . . . . . .63

x SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Special Commands in the Commands Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Chapter 5 Diagnostic Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99

Chapter 6 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107

Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xi

Chapter 8 Replaceable Parts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .145

Appendix A Quick Reference Guides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .149

xii SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Safety and Special Notices

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xiii

IMPORTANT Alerts you to connections to the building ground.

IMPORTANT Alerts you to the correct operating or maintenance procedures needed to

Safety Precautions for the SpectraSYSTEM Autosampler

xiv SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Heavy Lifting Hazard

Good Laboratory Practices

Keeping Good Records

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xv

High-Pressure Systems and Leaks

xvi SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Y To contact Technical Support

Find software updates and utilities to download at mssupport.thermo.com.

Y To contact Customer Service for ordering information

Y To copy manuals from the Internet

Y To suggest changes to documentation or to Help

• Send an e-mail message to the Technical Publications Editor at

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide xvii

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide 1

Figure 2 shows the components of the autosampler's injection system.

2 SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

Fill position Inject position

Note The current version of the SpectraSYSTEM AS3000 autosampler includes a

The temperature-control unit maintains the temperature of the tray compartment

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide 3

Full-loop Injection Type

During a full-loop injection, the autosampler performs these tasks:

4 SpectraSYSTEM AS3000 Autosampler User Guide Thermo Scientific

3. Switches the injection valve to the fill position.

Pull-loop Injection Type

During a pull-loop injection, the autosampler performs the following tasks:

Thermo Scientific SpectraSYSTEM AS3000 Autosampler User Guide 5